From 9279330bde7c5dc2391a532e02c1671853549805 Mon Sep 17 00:00:00 2001
From: Jing Lu <48139543+DeerWhale@users.noreply.github.com>
Date: Thu, 11 Jul 2024 09:20:49 -0400
Subject: [PATCH 1/5] Logging - avoid the zero division warning (#2695)

* avoid the warning of division zero

* run black formatter
---
 tardis/plasma/properties/radiative_properties.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/tardis/plasma/properties/radiative_properties.py b/tardis/plasma/properties/radiative_properties.py
index 37170b5c9e6..a1b8d0a5d8e 100644
--- a/tardis/plasma/properties/radiative_properties.py
+++ b/tardis/plasma/properties/radiative_properties.py
@@ -86,10 +86,16 @@ def calculate(
             metastability, lines_upper_level_index
         )
 
-        stimulated_emission_factor = 1 - (
-            (g_lower * n_upper) / (g_upper * n_lower)
+        # In theory the factor should be 1 for n_lower = 0, but in practice the opacity is reduced to 0 anyway
+        stimulated_emission_factor = np.zeros(n_lower.shape, dtype=np.float64)
+
+        n_lower_zero_mask = n_lower == 0.0
+        stimulated_emission_factor[~n_lower_zero_mask] = 1 - (
+            (g_lower * n_upper)[~n_lower_zero_mask]
+            / (g_upper * n_lower)[~n_lower_zero_mask]
         )
-        stimulated_emission_factor[n_lower == 0.0] = 0.0
+
+        # the following line probably can be removed as well
         stimulated_emission_factor[
             np.isneginf(stimulated_emission_factor)
         ] = 0.0

From f8f664cafbb6ecf0a4a31b25a623a16704bc48a2 Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Thu, 11 Jul 2024 19:24:01 +0530
Subject: [PATCH 2/5] Add arm64 conda-lock file (#2667)

* Add osx-arm64 conda lock file

* Temporary: Modify tests workflow to run tests using the arm lockfile, since macos-latest uses arm

* Fix label

* Reset tests workflow to use lock file from master
---
 .github/workflows/tests.yml |    4 +-
 conda-lock.yml              | 4440 ++++++++++++++++++++++++++++++++++-
 conda-osx-arm64.lock        |  313 +++
 3 files changed, 4701 insertions(+), 56 deletions(-)
 create mode 100644 conda-osx-arm64.lock

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 515ddc294c7..5e12f9ebbdb 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -39,9 +39,9 @@ jobs:
     strategy:
       matrix:
         pip: [true, false]
-        label: [osx-64, linux-64]
+        label: [osx-arm64, linux-64]
         include:
-          - label: osx-64
+          - label: osx-arm64
             os: macos-latest
             prefix: /Users/runner/miniconda3/envs/tardis
 
diff --git a/conda-lock.yml b/conda-lock.yml
index 3be364b974e..971bf7ef6df 100644
--- a/conda-lock.yml
+++ b/conda-lock.yml
@@ -15,12 +15,14 @@ metadata:
   content_hash:
     osx-64: f53de271de36e87ab6e9f5fa06dd1d75afde77a9406afae73f896a5ec1cdffcf
     linux-64: eb19f5b22e0784cf376dc551616a0294a2f7c0c5f0238c888619e1797240a813
+    osx-arm64: 8ba187f2338166be0b68427778ce769206c349bcbd0beeb7cc4b16ec73fd0186
   channels:
   - url: conda-forge
     used_env_vars: []
   platforms:
   - linux-64
   - osx-64
+  - osx-arm64
   sources:
   - tardis_env3.yml
   - /Users/wkerzend/python/tardis/tardis_env3.yml
@@ -74,6 +76,18 @@ package:
     sha256: fd39ad2fabec1569bbb0dfdae34ab6ce7de6ec09dcec8638f83dad0373594069
   category: main
   optional: false
+- name: alabaster
+  version: 0.7.16
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.9'
+  url: https://conda.anaconda.org/conda-forge/noarch/alabaster-0.7.16-pyhd8ed1ab_0.conda
+  hash:
+    md5: def531a3ac77b7fb8c21d17bb5d0badb
+    sha256: fd39ad2fabec1569bbb0dfdae34ab6ce7de6ec09dcec8638f83dad0373594069
+  category: main
+  optional: false
 - name: anyio
   version: 4.4.0
   manager: conda
@@ -106,6 +120,22 @@ package:
     sha256: 84ac9429812495f12939ab4994f2634f7cacd254f6234a0c2c0243daed15a7ee
   category: main
   optional: false
+- name: anyio
+  version: 4.4.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    exceptiongroup: '>=1.0.2'
+    idna: '>=2.8'
+    python: '>=3.8'
+    sniffio: '>=1.1'
+    typing_extensions: '>=4.1'
+  url: https://conda.anaconda.org/conda-forge/noarch/anyio-4.4.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 1fa97c6e8db1f82c64ff17a5efc4ae8e
+    sha256: 84ac9429812495f12939ab4994f2634f7cacd254f6234a0c2c0243daed15a7ee
+  category: main
+  optional: false
 - name: appnope
   version: 0.1.4
   manager: conda
@@ -118,6 +148,18 @@ package:
     sha256: 45ae2d41f4a4dcf8707633d3d7ae376fc62f0c09b1d063c3049c3f6f8c911670
   category: main
   optional: false
+- name: appnope
+  version: 0.1.4
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.7'
+  url: https://conda.anaconda.org/conda-forge/noarch/appnope-0.1.4-pyhd8ed1ab_0.conda
+  hash:
+    md5: cc4834a9ee7cc49ce8d25177c47b10d8
+    sha256: 45ae2d41f4a4dcf8707633d3d7ae376fc62f0c09b1d063c3049c3f6f8c911670
+  category: main
+  optional: false
 - name: argon2-cffi
   version: 23.1.0
   manager: conda
@@ -146,6 +188,20 @@ package:
     sha256: 130766446f5507bd44df957b6b5c898a8bd98f024bb426ed6cb9ff1ad67fc677
   category: main
   optional: false
+- name: argon2-cffi
+  version: 23.1.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    argon2-cffi-bindings: ''
+    python: '>=3.7'
+    typing-extensions: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-23.1.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 3afef1f55a1366b4d3b6a0d92e2235e4
+    sha256: 130766446f5507bd44df957b6b5c898a8bd98f024bb426ed6cb9ff1ad67fc677
+  category: main
+  optional: false
 - name: argon2-cffi-bindings
   version: 21.2.0
   manager: conda
@@ -175,6 +231,20 @@ package:
     sha256: aa321e91f0ff365b5261fa1dcffa2d32aa957561bdbb38988e52e28e25a762a8
   category: main
   optional: false
+- name: argon2-cffi-bindings
+  version: 21.2.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    cffi: '>=1.0.1'
+    python: '>=3.12.0rc3,<3.13.0a0'
+    python_abi: 3.12.*
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/argon2-cffi-bindings-21.2.0-py312h02f2b3b_4.conda
+  hash:
+    md5: 015edbb6fae68ab35881f55f149d4725
+    sha256: 1cfcf4b2d36a3b183a5cb1c69f85768166e50af6ced5ae381c440666a6da12c6
+  category: main
+  optional: false
 - name: arrow
   version: 1.3.0
   manager: conda
@@ -203,6 +273,20 @@ package:
     sha256: ff49825c7f9e29e09afa6284300810e7a8640d621740efb47c4541f4dc4969db
   category: main
   optional: false
+- name: arrow
+  version: 1.3.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.8'
+    python-dateutil: '>=2.7.0'
+    types-python-dateutil: '>=2.8.10'
+  url: https://conda.anaconda.org/conda-forge/noarch/arrow-1.3.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: b77d8c2313158e6e461ca0efb1c2c508
+    sha256: ff49825c7f9e29e09afa6284300810e7a8640d621740efb47c4541f4dc4969db
+  category: main
+  optional: false
 - name: astropy
   version: 6.1.1
   manager: conda
@@ -243,6 +327,26 @@ package:
     sha256: f6724466cefbc25a02c2e4727ccb2ec89004a566a6a12f74d9619af082ba08d4
   category: main
   optional: false
+- name: astropy
+  version: 6.1.1
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    __osx: '>=11.0'
+    astropy-iers-data: '>=0.2024.5.27.0.30.8'
+    importlib-metadata: ''
+    numpy: '>=1.23'
+    packaging: '>=19.0'
+    pyerfa: '>=2.0.1.1'
+    python: '>=3.12,<3.13.0a0'
+    python_abi: 3.12.*
+    pyyaml: '>=3.13'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/astropy-6.1.1-py312hbebd99a_0.conda
+  hash:
+    md5: 2e3e09291e0ff4857df0826bbaac1ffa
+    sha256: a055e4b63f18e2f164f90ac49e8228d983b971b8de54ba29706647bb294d76ec
+  category: main
+  optional: false
 - name: astropy-iers-data
   version: 0.2024.6.17.0.31.35
   manager: conda
@@ -267,6 +371,18 @@ package:
     sha256: 9f49dfdedc4c34a5283d8c81397be6cd2a2c3de09501b8fb0d45b0fb6d51e643
   category: main
   optional: false
+- name: astropy-iers-data
+  version: 0.2024.6.17.0.31.35
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.8'
+  url: https://conda.anaconda.org/conda-forge/noarch/astropy-iers-data-0.2024.6.17.0.31.35-pyhd8ed1ab_0.conda
+  hash:
+    md5: f535beec9185f435fd331ad9f7c47099
+    sha256: 9f49dfdedc4c34a5283d8c81397be6cd2a2c3de09501b8fb0d45b0fb6d51e643
+  category: main
+  optional: false
 - name: astropy-sphinx-theme
   version: '1.1'
   manager: conda
@@ -293,6 +409,19 @@ package:
     sha256: 9abe1756535ddc105c32b8746f98f4ae6f90523d46a50afa542415a358c9093b
   category: main
   optional: false
+- name: astropy-sphinx-theme
+  version: '1.1'
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.7'
+    setuptools: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/astropy-sphinx-theme-1.1-pyhd8ed1ab_0.conda
+  hash:
+    md5: 9941dc6d227213c20be1a1f45bdf1102
+    sha256: 9abe1756535ddc105c32b8746f98f4ae6f90523d46a50afa542415a358c9093b
+  category: main
+  optional: false
 - name: asttokens
   version: 2.4.1
   manager: conda
@@ -319,6 +448,19 @@ package:
     sha256: 708168f026df19a0344983754d27d1f7b28bb21afc7b97a82f02c4798a3d2111
   category: main
   optional: false
+- name: asttokens
+  version: 2.4.1
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.5'
+    six: '>=1.12.0'
+  url: https://conda.anaconda.org/conda-forge/noarch/asttokens-2.4.1-pyhd8ed1ab_0.conda
+  hash:
+    md5: 5f25798dcefd8252ce5f9dc494d5f571
+    sha256: 708168f026df19a0344983754d27d1f7b28bb21afc7b97a82f02c4798a3d2111
+  category: main
+  optional: false
 - name: async-lru
   version: 2.0.4
   manager: conda
@@ -345,6 +487,19 @@ package:
     sha256: 7ed83731979fe5b046c157730e50af0e24454468bbba1ed8fc1a3107db5d7518
   category: main
   optional: false
+- name: async-lru
+  version: 2.0.4
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.8'
+    typing_extensions: '>=4.0.0'
+  url: https://conda.anaconda.org/conda-forge/noarch/async-lru-2.0.4-pyhd8ed1ab_0.conda
+  hash:
+    md5: 3d081de3a6ea9f894bbb585e8e3a4dcb
+    sha256: 7ed83731979fe5b046c157730e50af0e24454468bbba1ed8fc1a3107db5d7518
+  category: main
+  optional: false
 - name: atk-1.0
   version: 2.38.0
   manager: conda
@@ -374,6 +529,21 @@ package:
     sha256: a5972a943764e46478c966b26be61de70dcd7d0cfda4bd0b0c46916ae32e0492
   category: main
   optional: false
+- name: atk-1.0
+  version: 2.38.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    __osx: '>=11.0'
+    libcxx: '>=16'
+    libglib: '>=2.80.0,<3.0a0'
+    libintl: '>=0.22.5,<1.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/atk-1.0-2.38.0-hd03087b_2.conda
+  hash:
+    md5: 57301986d02d30d6805fdce6c99074ee
+    sha256: b0747f9b1bc03d1932b4d8c586f39a35ac97e7e72fe6e63f2b2a2472d466f3c1
+  category: main
+  optional: false
 - name: attrs
   version: 23.2.0
   manager: conda
@@ -398,6 +568,18 @@ package:
     sha256: 77c7d03bdb243a048fff398cedc74327b7dc79169ebe3b4c8448b0331ea55fea
   category: main
   optional: false
+- name: attrs
+  version: 23.2.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.7'
+  url: https://conda.anaconda.org/conda-forge/noarch/attrs-23.2.0-pyh71513ae_0.conda
+  hash:
+    md5: 5e4c0743c70186509d1412e03c2d8dfa
+    sha256: 77c7d03bdb243a048fff398cedc74327b7dc79169ebe3b4c8448b0331ea55fea
+  category: main
+  optional: false
 - name: babel
   version: 2.14.0
   manager: conda
@@ -426,6 +608,20 @@ package:
     sha256: 8584e3da58e92b72641c89ff9b98c51f0d5dbe76e527867804cbdf03ac91d8e6
   category: main
   optional: false
+- name: babel
+  version: 2.14.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.7'
+    pytz: ''
+    setuptools: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/babel-2.14.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 9669586875baeced8fc30c0826c3270e
+    sha256: 8584e3da58e92b72641c89ff9b98c51f0d5dbe76e527867804cbdf03ac91d8e6
+  category: main
+  optional: false
 - name: beautifulsoup4
   version: 4.12.3
   manager: conda
@@ -452,6 +648,19 @@ package:
     sha256: 7b05b2d0669029326c623b9df7a29fa49d1982a9e7e31b2fea34b4c9a4a72317
   category: main
   optional: false
+- name: beautifulsoup4
+  version: 4.12.3
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.6'
+    soupsieve: '>=1.2'
+  url: https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.12.3-pyha770c72_0.conda
+  hash:
+    md5: 332493000404d8411859539a5a630865
+    sha256: 7b05b2d0669029326c623b9df7a29fa49d1982a9e7e31b2fea34b4c9a4a72317
+  category: main
+  optional: false
 - name: black
   version: 22.3.0
   manager: conda
@@ -492,6 +701,26 @@ package:
     sha256: bbf97913b074a5fc71b5c4a50472e0e863b1abc564d1c73d79262d4557256960
   category: main
   optional: false
+- name: black
+  version: 22.3.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    click: '>=8.0.0'
+    dataclasses: '>=0.6'
+    mypy_extensions: '>=0.4.3'
+    pathspec: '>=0.9,<1'
+    platformdirs: '>=2'
+    python: '>=3.6'
+    tomli: '>=1.1.0'
+    typed-ast: '>=1.4.2'
+    typing_extensions: '>=3.10,!=3.10.0.1'
+  url: https://conda.anaconda.org/conda-forge/noarch/black-22.3.0-pyhd8ed1ab_0.tar.bz2
+  hash:
+    md5: 7ecbfaae9a30b73c1a6e36e4a0debc03
+    sha256: bbf97913b074a5fc71b5c4a50472e0e863b1abc564d1c73d79262d4557256960
+  category: main
+  optional: false
 - name: bleach
   version: 6.1.0
   manager: conda
@@ -524,6 +753,22 @@ package:
     sha256: 845e77ef495376c5c3c328ccfd746ca0ef1978150cae8eae61a300fe7755fb08
   category: main
   optional: false
+- name: bleach
+  version: 6.1.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    packaging: ''
+    python: '>=3.6'
+    setuptools: ''
+    six: '>=1.9.0'
+    webencodings: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/bleach-6.1.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 0ed9d7c0e9afa7c025807a9a8136ea3e
+    sha256: 845e77ef495376c5c3c328ccfd746ca0ef1978150cae8eae61a300fe7755fb08
+  category: main
+  optional: false
 - name: blosc
   version: 1.21.5
   manager: conda
@@ -558,6 +803,23 @@ package:
     sha256: a2e867d61ce398187d59f59e034e8651c825cb33224d2c6f315876b6df5e2161
   category: main
   optional: false
+- name: blosc
+  version: 1.21.5
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    __osx: '>=11.0'
+    libcxx: '>=16'
+    libzlib: '>=1.2.13,<2.0.0a0'
+    lz4-c: '>=1.9.3,<1.10.0a0'
+    snappy: '>=1.2.0,<1.3.0a0'
+    zstd: '>=1.5.5,<1.6.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/blosc-1.21.5-h9c252e8_1.conda
+  hash:
+    md5: e1be80625e4f6bdc2154ee099c641683
+    sha256: 3b38493b95cc3d9f6369bbcbab55a2cdbbe6bbe32c74b923f8d638e874033139
+  category: main
+  optional: false
 - name: brotli
   version: 1.1.0
   manager: conda
@@ -587,6 +849,20 @@ package:
     sha256: 4bf66d450be5d3f9ebe029b50f818d088b1ef9666b1f19e90c85479c77bbdcde
   category: main
   optional: false
+- name: brotli
+  version: 1.1.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    brotli-bin: 1.1.0
+    libbrotlidec: 1.1.0
+    libbrotlienc: 1.1.0
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/brotli-1.1.0-hb547adb_1.conda
+  hash:
+    md5: a33aa58d448cbc054f887e39dd1dfaea
+    sha256: 62d1587deab752fcee07adc371eb20fcadc09f72c0c85399c22b637ca858020f
+  category: main
+  optional: false
 - name: brotli-bin
   version: 1.1.0
   manager: conda
@@ -614,6 +890,19 @@ package:
     sha256: 7ca3cfb4c5df314ed481301335387ab2b2ee651e2c74fbb15bacc795c664a5f1
   category: main
   optional: false
+- name: brotli-bin
+  version: 1.1.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    libbrotlidec: 1.1.0
+    libbrotlienc: 1.1.0
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/brotli-bin-1.1.0-hb547adb_1.conda
+  hash:
+    md5: 990d04f8c017b1b77103f9a7730a5f12
+    sha256: 8fbfc2834606292016f2faffac67deea4c5cdbc21a61169f0b355e1600105a24
+  category: main
+  optional: false
 - name: brotli-python
   version: 1.1.0
   manager: conda
@@ -643,6 +932,20 @@ package:
     sha256: fc55988f9bc05a938ea4b8c20d6545bed6e9c6c10aa5147695f981136ca894c1
   category: main
   optional: false
+- name: brotli-python
+  version: 1.1.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    libcxx: '>=15.0.7'
+    python: '>=3.12.0rc3,<3.13.0a0'
+    python_abi: 3.12.*
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/brotli-python-1.1.0-py312h9f69965_1.conda
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-- name: exceptiongroup
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   category: main
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   category: main
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/expat-2.6.2-hebf3989_0.conda
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   category: main
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+- name: font-ttf-dejavu-sans-mono
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+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
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   category: main
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+- name: font-ttf-inconsolata
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+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
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   category: main
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+- name: font-ttf-source-code-pro
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+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
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   category: main
   optional: false
+- name: font-ttf-ubuntu
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+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda
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   category: main
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+    freetype: '>=2.12.1,<3.0a0'
+    libzlib: '>=1.2.13,<2.0.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/fontconfig-2.14.2-h82840c6_0.conda
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 - name: fonts-conda-ecosystem
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   category: main
   optional: false
+- name: fonts-conda-ecosystem
+  version: '1'
+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
+  hash:
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 - name: fonts-conda-forge
   version: '1'
   manager: conda
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   category: main
   optional: false
+- name: fonts-conda-forge
+  version: '1'
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    font-ttf-dejavu-sans-mono: ''
+    font-ttf-inconsolata: ''
+    font-ttf-source-code-pro: ''
+    font-ttf-ubuntu: ''
+  url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
+  hash:
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   category: main
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+- name: fonttools
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+  platform: osx-arm64
+  dependencies:
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+    brotli: ''
+    munkres: ''
+    python: '>=3.12,<3.13.0a0'
+    python_abi: 3.12.*
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/fonttools-4.53.0-py312h7e5086c_0.conda
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   category: main
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+- name: fqdn
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+    python: '>=2.7,<4'
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+  hash:
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   category: main
   optional: false
+- name: freetype
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+  platform: osx-arm64
+  dependencies:
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+    libzlib: '>=1.2.13,<2.0.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/freetype-2.12.1-hadb7bae_2.conda
+  hash:
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   category: main
   optional: false
+- name: fribidi
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+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/fribidi-1.0.10-h27ca646_0.tar.bz2
+  hash:
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   category: main
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+- name: future
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+  platform: osx-arm64
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+  url: https://conda.anaconda.org/conda-forge/noarch/future-1.0.0-pyhd8ed1ab_0.conda
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   category: main
   optional: false
+- name: gdk-pixbuf
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+  manager: conda
+  platform: osx-arm64
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+    libglib: '>=2.80.2,<3.0a0'
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+    libtiff: '>=4.6.0,<4.7.0a0'
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   category: main
   optional: false
+- name: gettext
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+  manager: conda
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+    libasprintf: 0.22.5
+    libasprintf-devel: 0.22.5
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/gettext-0.22.5-h8fbad5d_2.conda
+  hash:
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 - name: gettext-tools
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   manager: conda
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   category: main
   optional: false
+- name: gettext-tools
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    libiconv: '>=1.17,<2.0a0'
+    libintl: 0.22.5
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/gettext-tools-0.22.5-h8fbad5d_2.conda
+  hash:
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   category: main
   optional: false
+- name: giflib
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+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/giflib-5.2.2-h93a5062_0.conda
+  hash:
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   category: main
   optional: false
+- name: git-lfs
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+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/git-lfs-3.5.1-hce30654_0.conda
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   category: main
   optional: false
+- name: gmp
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+  manager: conda
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+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/gmp-6.3.0-hebf3989_1.conda
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   category: main
   optional: false
+- name: gmpy2
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+  manager: conda
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+    gmp: '>=6.3.0,<7.0a0'
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+    mpfr: '>=4.2.1,<5.0a0'
+    python: '>=3.12,<3.13.0a0'
+    python_abi: 3.12.*
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   category: main
   optional: false
+- name: graphite2
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/graphite2-1.3.13-hebf3989_1003.conda
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 - name: graphviz
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   category: main
   optional: false
-- name: gtk2
-  version: 2.24.33
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   manager: conda
-  platform: linux-64
+  platform: osx-arm64
   dependencies:
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+    __osx: '>=11.0'
     cairo: '>=1.18.0,<2.0a0'
-    fontconfig: '>=2.14.2,<3.0a0'
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+    libzlib: '>=1.2.13,<2.0.0a0'
+    pango: '>=1.50.14,<2.0a0'
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+    cairo: '>=1.18.0,<2.0a0'
+    fontconfig: '>=2.14.2,<3.0a0'
     fonts-conda-ecosystem: ''
     freetype: '>=2.12.1,<3.0a0'
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   category: main
   optional: false
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+  manager: conda
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+    cairo: '>=1.18.0,<2.0a0'
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+    libglib: '>=2.78.4,<3.0a0'
+    pango: '>=1.50.14,<2.0a0'
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   category: main
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+- name: httpcore
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+    certifi: ''
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+    python: '>=3.8'
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   category: main
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   category: main
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   category: main
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+- name: icu
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   category: main
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+- name: idna
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   category: main
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   category: main
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   category: main
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+  url: https://conda.anaconda.org/conda-forge/noarch/importlib_metadata-7.1.0-hd8ed1ab_0.conda
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   category: main
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   category: main
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+  url: https://conda.anaconda.org/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_0.conda
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   category: main
   optional: false
-- name: ipython
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   manager: conda
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+  platform: osx-arm64
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-    typing_extensions: '>=4.6'
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+    tornado: '>=6.1'
+    traitlets: '>=5.4.0'
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   url: https://conda.anaconda.org/conda-forge/noarch/ipython-8.25.0-pyh707e725_0.conda
   hash:
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   category: main
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   category: main
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+- name: ipython_genutils
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+  url: https://conda.anaconda.org/conda-forge/noarch/ipython_genutils-0.2.0-pyhd8ed1ab_1.conda
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   category: main
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   category: main
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   category: main
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+- name: jedi
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+    python: '>=3.6'
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   category: main
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   category: main
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+    openssl: '>=3.2.0,<4.0a0'
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   category: main
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   category: main
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   category: main
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   category: main
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   category: main
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   category: main
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   category: main
   optional: false
+- name: libxcb
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 - name: libxcrypt
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   category: main
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   category: main
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+- name: libzlib
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/libzlib-1.3.1-hfb2fe0b_1.conda
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   category: main
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   category: main
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/llvmlite-0.42.0-py312h17030e7_1.conda
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   category: main
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   category: main
   optional: false
+- name: lz4-c
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   category: main
   optional: false
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+    python_abi: 3.12.*
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   category: main
   optional: false
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   manager: conda
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   url: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.1.7-pyhd8ed1ab_0.conda
   hash:
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   manager: conda
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   url: https://conda.anaconda.org/conda-forge/noarch/matplotlib-inline-0.1.7-pyhd8ed1ab_0.conda
   hash:
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   category: main
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   category: main
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+- name: ncurses
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+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/ncurses-6.5-hb89a1cb_0.conda
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   category: main
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+- name: nest-asyncio
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+  dependencies:
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   category: main
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+- name: networkx
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   category: main
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+    python: '>=3.7'
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     python_abi: 3.12.*
-  url: https://conda.anaconda.org/conda-forge/osx-64/numba-0.59.1-py312h04e34b5_0.conda
+  url: https://conda.anaconda.org/conda-forge/osx-64/numba-0.59.1-py312h04e34b5_0.conda
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   hash:
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   category: main
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+- name: numexpr
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   category: main
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   category: main
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+- name: numpydoc
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   category: main
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   category: main
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   category: main
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   category: main
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+    tenacity: '>=6.2.0'
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   category: main
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   category: main
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   category: main
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   category: main
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   category: main
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+    python: '>=3.12,<3.13.0a0'
+    python_abi: 3.12.*
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+- name: radioactivedecay
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+    python: '>=3.8'
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+    python: '>=3.8'
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+- name: requests
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+  url: https://conda.anaconda.org/conda-forge/noarch/rfc3339-validator-0.1.4-pyhd8ed1ab_0.tar.bz2
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     six: ''
+    python: '>=3.5'
   url: https://conda.anaconda.org/conda-forge/noarch/rfc3339-validator-0.1.4-pyhd8ed1ab_0.tar.bz2
   hash:
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   manager: conda
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+  platform: osx-arm64
   dependencies:
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   url: https://conda.anaconda.org/conda-forge/noarch/rfc3339-validator-0.1.4-pyhd8ed1ab_0.tar.bz2
   hash:
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   category: main
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+- name: rfc3986-validator
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+  url: https://conda.anaconda.org/conda-forge/noarch/rfc3986-validator-0.1.1-pyh9f0ad1d_0.tar.bz2
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   category: main
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+- name: rpds-py
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+- name: ruff
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   category: main
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/scipy-1.13.1-py312h14ffa8f_0.conda
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   category: main
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+    pyobjc-framework-cocoa: ''
+    python: '>=3.7'
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   category: main
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   category: main
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+  url: https://conda.anaconda.org/conda-forge/noarch/setuptools_scm-8.1.0-hd8ed1ab_0.conda
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   category: main
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+- name: six
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2
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   category: main
   optional: false
+- name: snakeviz
+  version: 2.2.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+    tornado: '>=2.0'
+  url: https://conda.anaconda.org/conda-forge/noarch/snakeviz-2.2.0-pyhd8ed1ab_0.conda
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   category: main
   optional: false
+- name: snappy
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/osx-arm64/snappy-1.2.0-hd04f947_1.conda
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   category: main
   optional: false
+- name: sniffio
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.1-pyhd8ed1ab_0.conda
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   category: main
   optional: false
+- name: snowballstemmer
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/noarch/snowballstemmer-2.2.0-pyhd8ed1ab_0.tar.bz2
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   category: main
   optional: false
+- name: soupsieve
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.5-pyhd8ed1ab_1.conda
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   category: main
   optional: false
+- name: sphinx
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+    pygments: '>=2.14'
+    python: '>=3.9'
+    requests: '>=2.25.0'
+    snowballstemmer: '>=2.0'
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   category: main
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   category: main
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   category: main
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-  url: https://conda.anaconda.org/conda-forge/osx-64/tornado-6.4.1-py312hbd25219_0.conda
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/tornado-6.4.1-py312h7e5086c_0.conda
   hash:
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-    sha256: efba7cd7d5c311f57fd1a658c0f8ae65f9c5f3c9c41111a689dcad45407944c8
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     sha256: 75342f40a69e434a1a23003c3e254a95dca695fb14955bc32f1819cd503964b2
   category: main
   optional: false
+- name: tqdm
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+  dependencies:
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+    python: '>=3.7'
+  url: https://conda.anaconda.org/conda-forge/noarch/tqdm-4.66.4-pyhd8ed1ab_0.conda
+  hash:
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   category: main
   optional: false
+- name: traitlets
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+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/noarch/traitlets-5.14.3-pyhd8ed1ab_0.conda
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   category: main
   optional: false
+- name: typed-ast
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.12.0rc3,<3.13.0a0'
+    python_abi: 3.12.*
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/typed-ast-1.5.5-py312h02f2b3b_1.conda
+  hash:
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+    sha256: d5a43f7d2011d39f0e235016ed330ca6f669e525045775036ff7bc1223afd7f0
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 - name: types-python-dateutil
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     sha256: 6630bbc43dfb72339fadafc521db56c9d17af72bfce459af195eecb01163de20
   category: main
   optional: false
+- name: types-python-dateutil
+  version: 2.9.0.20240316
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.6'
+  url: https://conda.anaconda.org/conda-forge/noarch/types-python-dateutil-2.9.0.20240316-pyhd8ed1ab_0.conda
+  hash:
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 - name: typing-extensions
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   category: main
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+- name: typing-extensions
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
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+  url: https://conda.anaconda.org/conda-forge/noarch/typing-extensions-4.12.2-hd8ed1ab_0.conda
+  hash:
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+    sha256: d3b9a8ed6da7c9f9553c5fd8a4fca9c3e0ab712fa5f497859f82337d67533b73
+  category: main
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 - name: typing_extensions
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     sha256: 0fce54f8ec3e59f5ef3bb7641863be4e1bf1279623e5af3d3fa726e8f7628ddb
   category: main
   optional: false
+- name: typing_extensions
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+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.8'
+  url: https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.12.2-pyha770c72_0.conda
+  hash:
+    md5: ebe6952715e1d5eb567eeebf25250fa7
+    sha256: 0fce54f8ec3e59f5ef3bb7641863be4e1bf1279623e5af3d3fa726e8f7628ddb
+  category: main
+  optional: false
 - name: typing_utils
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     sha256: 9e3758b620397f56fb709f796969de436d63b7117897159619b87938e1f78739
   category: main
   optional: false
+- name: typing_utils
+  version: 0.1.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.6.1'
+  url: https://conda.anaconda.org/conda-forge/noarch/typing_utils-0.1.0-pyhd8ed1ab_0.tar.bz2
+  hash:
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+    sha256: 9e3758b620397f56fb709f796969de436d63b7117897159619b87938e1f78739
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+  optional: false
 - name: tzdata
   version: 2024a
   manager: conda
@@ -8321,6 +12435,17 @@ package:
     sha256: 7b2b69c54ec62a243eb6fba2391b5e443421608c3ae5dbff938ad33ca8db5122
   category: main
   optional: false
+- name: tzdata
+  version: 2024a
+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda
+  hash:
+    md5: 161081fc7cec0bfda0d86d7cb595f8d8
+    sha256: 7b2b69c54ec62a243eb6fba2391b5e443421608c3ae5dbff938ad33ca8db5122
+  category: main
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 - name: uri-template
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@@ -8345,6 +12470,18 @@ package:
     sha256: b76904b53721dc88a46352324c79d2b077c2f74a9f7208ad2c4249892669ae94
   category: main
   optional: false
+- name: uri-template
+  version: 1.3.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.7'
+  url: https://conda.anaconda.org/conda-forge/noarch/uri-template-1.3.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 0944dc65cb4a9b5b68522c3bb585d41c
+    sha256: b76904b53721dc88a46352324c79d2b077c2f74a9f7208ad2c4249892669ae94
+  category: main
+  optional: false
 - name: urllib3
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   manager: conda
@@ -8373,6 +12510,20 @@ package:
     sha256: 8cd972048f297b8e0601158ce352f5ca9510dda9f2706a46560220aa58b9f038
   category: main
   optional: false
+- name: urllib3
+  version: 2.2.2
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    brotli-python: '>=1.0.9'
+    pysocks: '>=1.5.6,<2.0,!=1.5.7'
+    python: '>=3.7'
+  url: https://conda.anaconda.org/conda-forge/noarch/urllib3-2.2.2-pyhd8ed1ab_0.conda
+  hash:
+    md5: 92cdb6fe54b78739ad70637e4f0deb07
+    sha256: 8cd972048f297b8e0601158ce352f5ca9510dda9f2706a46560220aa58b9f038
+  category: main
+  optional: false
 - name: wcwidth
   version: 0.2.13
   manager: conda
@@ -8397,6 +12548,18 @@ package:
     sha256: b6cd2fee7e728e620ec736d8dfee29c6c9e2adbd4e695a31f1d8f834a83e57e3
   category: main
   optional: false
+- name: wcwidth
+  version: 0.2.13
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.8'
+  url: https://conda.anaconda.org/conda-forge/noarch/wcwidth-0.2.13-pyhd8ed1ab_0.conda
+  hash:
+    md5: 68f0738df502a14213624b288c60c9ad
+    sha256: b6cd2fee7e728e620ec736d8dfee29c6c9e2adbd4e695a31f1d8f834a83e57e3
+  category: main
+  optional: false
 - name: webcolors
   version: 24.6.0
   manager: conda
@@ -8421,6 +12584,18 @@ package:
     sha256: 6377de3bc05b80f25c5fe75f180a81fc8a6aa601d4b228161f75f78862d00a0f
   category: main
   optional: false
+- name: webcolors
+  version: 24.6.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.5'
+  url: https://conda.anaconda.org/conda-forge/noarch/webcolors-24.6.0-pyhd8ed1ab_0.conda
+  hash:
+    md5: 419f2f6cf90fc7a6feee657752cd0f7b
+    sha256: 6377de3bc05b80f25c5fe75f180a81fc8a6aa601d4b228161f75f78862d00a0f
+  category: main
+  optional: false
 - name: webencodings
   version: 0.5.1
   manager: conda
@@ -8445,6 +12620,18 @@ package:
     sha256: 2adf9bd5482802837bc8814cbe28d7b2a4cbd2e2c52e381329eaa283b3ed1944
   category: main
   optional: false
+- name: webencodings
+  version: 0.5.1
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=2.6'
+  url: https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-pyhd8ed1ab_2.conda
+  hash:
+    md5: daf5160ff9cde3a468556965329085b9
+    sha256: 2adf9bd5482802837bc8814cbe28d7b2a4cbd2e2c52e381329eaa283b3ed1944
+  category: main
+  optional: false
 - name: websocket-client
   version: 1.8.0
   manager: conda
@@ -8469,6 +12656,18 @@ package:
     sha256: 44a5e3b97feef24cd719f7851cca9af9799dc9c17d3e0298d5856baab2d682f5
   category: main
   optional: false
+- name: websocket-client
+  version: 1.8.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.8'
+  url: https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.8.0-pyhd8ed1ab_0.conda
+  hash:
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+    sha256: 44a5e3b97feef24cd719f7851cca9af9799dc9c17d3e0298d5856baab2d682f5
+  category: main
+  optional: false
 - name: wheel
   version: 0.43.0
   manager: conda
@@ -8493,6 +12692,18 @@ package:
     sha256: cb318f066afd6fd64619f14c030569faf3f53e6f50abf743b4c865e7d95b96bc
   category: main
   optional: false
+- name: wheel
+  version: 0.43.0
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.8'
+  url: https://conda.anaconda.org/conda-forge/noarch/wheel-0.43.0-pyhd8ed1ab_1.conda
+  hash:
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+    sha256: cb318f066afd6fd64619f14c030569faf3f53e6f50abf743b4c865e7d95b96bc
+  category: main
+  optional: false
 - name: widgetsnbextension
   version: 3.6.6
   manager: conda
@@ -8519,6 +12730,19 @@ package:
     sha256: 5fb8ac32fb9d5b2860d271ae1959aa6953044f06cbe5e54d912125cca27dda3b
   category: main
   optional: false
+- name: widgetsnbextension
+  version: 3.6.6
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    notebook: '>=4.4.1'
+    python: '>=3.7'
+  url: https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda
+  hash:
+    md5: fe79dfe7d51794d665ec3c2fdd4e47c3
+    sha256: 5fb8ac32fb9d5b2860d271ae1959aa6953044f06cbe5e54d912125cca27dda3b
+  category: main
+  optional: false
 - name: xorg-kbproto
   version: 1.0.7
   manager: conda
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     sha256: 8a2e398c4f06f10c64e69f56bcf3ddfa30b432201446a0893505e735b346619a
   category: main
   optional: false
+- name: xorg-libxau
+  version: 1.0.11
+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxau-1.0.11-hb547adb_0.conda
+  hash:
+    md5: ca73dc4f01ea91e44e3ed76602c5ea61
+    sha256: 02c313a1cada46912e5b9bdb355cfb4534bfe22143b4ea4ecc419690e793023b
+  category: main
+  optional: false
 - name: xorg-libxdmcp
   version: 1.1.3
   manager: conda
@@ -8619,6 +12854,17 @@ package:
     sha256: 485421c16f03a01b8ed09984e0b2ababdbb3527e1abf354ff7646f8329be905f
   category: main
   optional: false
+- name: xorg-libxdmcp
+  version: 1.1.3
+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/xorg-libxdmcp-1.1.3-h27ca646_0.tar.bz2
+  hash:
+    md5: 6738b13f7fadc18725965abdd4129c36
+    sha256: d9a2fb4762779994718832f05a7d62ab2dcf6103a312235267628b5187ce88f7
+  category: main
+  optional: false
 - name: xorg-libxext
   version: 1.3.4
   manager: conda
@@ -8706,6 +12952,17 @@ package:
     sha256: eb09823f34cc2dd663c0ec4ab13f246f45dcd52e5b8c47b9864361de5204a1c8
   category: main
   optional: false
+- name: xz
+  version: 5.2.6
+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/xz-5.2.6-h57fd34a_0.tar.bz2
+  hash:
+    md5: 39c6b54e94014701dd157f4f576ed211
+    sha256: 59d78af0c3e071021cfe82dc40134c19dab8cdf804324b62940f5c8cd71803ec
+  category: main
+  optional: false
 - name: yaml
   version: 0.2.5
   manager: conda
@@ -8729,6 +12986,17 @@ package:
     sha256: 5301417e2c8dea45b401ffee8df3957d2447d4ce80c83c5ff151fc6bfe1c4148
   category: main
   optional: false
+- name: yaml
+  version: 0.2.5
+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/yaml-0.2.5-h3422bc3_2.tar.bz2
+  hash:
+    md5: 4bb3f014845110883a3c5ee811fd84b4
+    sha256: 93181a04ba8cfecfdfb162fc958436d868cc37db504c58078eab4c1a3e57fbb7
+  category: main
+  optional: false
 - name: zeromq
   version: 4.3.5
   manager: conda
@@ -8759,6 +13027,21 @@ package:
     sha256: 871625ce993e6c61649b14659a3d1d6011fbb242b7d6a25cadbc6300b2356f32
   category: main
   optional: false
+- name: zeromq
+  version: 4.3.5
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    __osx: '>=11.0'
+    krb5: '>=1.21.2,<1.22.0a0'
+    libcxx: '>=16'
+    libsodium: '>=1.0.18,<1.0.19.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/zeromq-4.3.5-hcc0f68c_4.conda
+  hash:
+    md5: 39fb79e7a7a880a03f82c1f2eb7f7c73
+    sha256: c22520d6d66a80f17c5f2b3719ad4a6ee809b210b8ac87d6f05ab98b94b3abda
+  category: main
+  optional: false
 - name: zipp
   version: 3.19.2
   manager: conda
@@ -8783,6 +13066,18 @@ package:
     sha256: e3e9c8501f581bfdc4700b83ea283395e237ec6b9b5cbfbedb556e1da6f4fdc9
   category: main
   optional: false
+- name: zipp
+  version: 3.19.2
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    python: '>=3.8'
+  url: https://conda.anaconda.org/conda-forge/noarch/zipp-3.19.2-pyhd8ed1ab_0.conda
+  hash:
+    md5: 49808e59df5535116f6878b2a820d6f4
+    sha256: e3e9c8501f581bfdc4700b83ea283395e237ec6b9b5cbfbedb556e1da6f4fdc9
+  category: main
+  optional: false
 - name: zlib
   version: 1.3.1
   manager: conda
@@ -8809,6 +13104,19 @@ package:
     sha256: 41bd5fef28b2755d637e3a8ea5c84010628392fbcf80c7e3d7370aaced7ee4fe
   category: main
   optional: false
+- name: zlib
+  version: 1.3.1
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    __osx: '>=11.0'
+    libzlib: 1.3.1
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-1.3.1-hfb2fe0b_1.conda
+  hash:
+    md5: f27e021db7862b6ddbc1d3578f10d883
+    sha256: 87360c2dc662916aac37cf01e53324b4f4f78db6f399220818076752b093ede5
+  category: main
+  optional: false
 - name: zlib-ng
   version: 2.0.7
   manager: conda
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     sha256: 701bf17f3e22c7ba24ca547ccf4b2b5b4b58eda579ddaf68c0571427b10aa366
   category: main
   optional: false
+- name: zlib-ng
+  version: 2.0.7
+  manager: conda
+  platform: osx-arm64
+  dependencies: {}
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/zlib-ng-2.0.7-h1a8c8d9_0.conda
+  hash:
+    md5: 4852d8981e833f34c8ed32e4fb8e103b
+    sha256: c526e4b6351e351c89ed0c60ca43b9f04668363a58e355583dc7701efb4fca89
+  category: main
+  optional: false
 - name: zstd
   version: 1.5.6
   manager: conda
@@ -8859,3 +13178,16 @@ package:
     sha256: efa04a98cb149643fa54c4dad5a0179e36a5fbc88427ea0eec88ceed87fd0f96
   category: main
   optional: false
+- name: zstd
+  version: 1.5.6
+  manager: conda
+  platform: osx-arm64
+  dependencies:
+    __osx: '>=11.0'
+    libzlib: '>=1.2.13,<2.0.0a0'
+  url: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda
+  hash:
+    md5: d96942c06c3e84bfcc5efb038724a7fd
+    sha256: 2d4fd1ff7ee79cd954ca8e81abf11d9d49954dd1fef80f27289e2402ae9c2e09
+  category: main
+  optional: false
diff --git a/conda-osx-arm64.lock b/conda-osx-arm64.lock
new file mode 100644
index 00000000000..fb6e1a12302
--- /dev/null
+++ b/conda-osx-arm64.lock
@@ -0,0 +1,313 @@
+# Generated by conda-lock.
+# platform: osx-arm64
+# input_hash: 8ba187f2338166be0b68427778ce769206c349bcbd0beeb7cc4b16ec73fd0186
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/osx-arm64/bzip2-1.0.8-h93a5062_5.conda#1bbc659ca658bfd49a481b5ef7a0f40f
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+https://conda.anaconda.org/conda-forge/noarch/isoduration-20.11.0-pyhd8ed1ab_0.tar.bz2#4cb68948e0b8429534380243d063a27a
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-4.22.0-pyhd8ed1ab_0.conda#b9661a4b1200d6bc7d8a4cdafdc91468
+https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.6.2-pyhd8ed1ab_0.conda#3cdbb2fa84490e5fd44c9f9806c0d292
+https://conda.anaconda.org/conda-forge/osx-arm64/numpy-1.26.4-py312h8442bc7_0.conda#d83fc83d589e2625a3451c9a7e21047c
+https://conda.anaconda.org/conda-forge/osx-arm64/pango-1.54.0-h5cb9fbc_0.conda#e490cbccf161da2220fd9be3463c0fac
+https://conda.anaconda.org/conda-forge/osx-arm64/pybtex-docutils-1.0.3-py312h81bd7bf_1.conda#b2c19509bdc0242a61e1f9cd3553beb0
+https://conda.anaconda.org/conda-forge/noarch/pytest-html-4.1.1-pyhd8ed1ab_0.conda#4d2040212307d18392a2687772b3a96d
+https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.3-pyh31c8845_0.conda#c3cb67fc72fb38020fe7923dbbcf69b0
+https://conda.anaconda.org/conda-forge/noarch/setuptools_scm-8.1.0-hd8ed1ab_0.conda#7ed7b077f6c6ebcb5fc66f23985df487
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-apidoc-0.3.0-py_1.tar.bz2#855b087883443abb10f5faf6eef40860
+https://conda.anaconda.org/conda-forge/osx-arm64/contourpy-1.2.1-py312h0fef576_0.conda#f825cced50aa6ae9f6ae158a49ecb68c
+https://conda.anaconda.org/conda-forge/osx-arm64/gtk2-2.24.33-h7895bb2_4.conda#9c1ba062d59f3f49a2d32d9611d72686
+https://conda.anaconda.org/conda-forge/osx-arm64/h5py-3.11.0-nompi_py312h903599c_102.conda#ed56b709d6e19626753894fc903b8ffe
+https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.29.4-pyh57ce528_0.conda#1e991f9ed4a81d3482d46edbeb54721a
+https://conda.anaconda.org/conda-forge/noarch/jsonschema-with-format-nongpl-4.22.0-pyhd8ed1ab_0.conda#32ab666927ee17b9468c2c72bbd7ba1b
+https://conda.anaconda.org/conda-forge/osx-arm64/librsvg-2.58.1-hbc281fb_0.conda#e642889ae7e977769f6d0328e2ec7497
+https://conda.anaconda.org/conda-forge/noarch/nbformat-5.10.4-pyhd8ed1ab_0.conda#0b57b5368ab7fc7cdc9e3511fa867214
+https://conda.anaconda.org/conda-forge/osx-arm64/numba-0.59.1-py312hbaff935_0.conda#e4b79ed152a0499e5ccfe660140aeca7
+https://conda.anaconda.org/conda-forge/osx-arm64/numexpr-2.10.0-py312h8ae5369_0.conda#52a038a2c531adb72b8b3056952b5d87
+https://conda.anaconda.org/conda-forge/osx-arm64/pandas-2.2.2-py312h8ae5369_1.conda#b38af0cd7ae3616c90a2511272385941
+https://conda.anaconda.org/conda-forge/osx-arm64/pyerfa-2.0.1.4-py312hbebd99a_1.conda#e7885deec93e16fdced3b4fba11db813
+https://conda.anaconda.org/conda-forge/osx-arm64/scipy-1.13.1-py312h14ffa8f_0.conda#0ef7359585e53bb3ff4539cf204f9c62
+https://conda.anaconda.org/conda-forge/osx-arm64/astropy-6.1.1-py312hbebd99a_0.conda#2e3e09291e0ff4857df0826bbaac1ffa
+https://conda.anaconda.org/conda-forge/osx-arm64/graphviz-11.0.0-h9bb9bc9_0.conda#c004a0e5dfbe0ce38af9ab4684abd236
+https://conda.anaconda.org/conda-forge/noarch/jupyter_events-0.10.0-pyhd8ed1ab_0.conda#ed45423c41b3da15ea1df39b1f80c2ca
+https://conda.anaconda.org/conda-forge/osx-arm64/matplotlib-base-3.8.4-py312h4479663_2.conda#e4c7e00cc31a921bb2541c10c3c58a8c
+https://conda.anaconda.org/conda-forge/noarch/nbclient-0.10.0-pyhd8ed1ab_0.conda#15b51397e0fe8ea7d7da60d83eb76ebc
+https://conda.anaconda.org/conda-forge/osx-arm64/pytables-3.9.2-py312hb622ae1_2.conda#0c8c7932ec76f439adaf0e35784ee539
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.16.4-pyhd8ed1ab_1.conda#e2d2abb421c13456a9a9f80272fdf543
+https://conda.anaconda.org/conda-forge/osx-arm64/pygraphviz-1.13-py312h5f4d302_1.conda#fd4b95cc009d28310e4cb3b090b8ac09
+https://conda.anaconda.org/conda-forge/noarch/radioactivedecay-0.5.1-pyhd8ed1ab_0.conda#9fc71a62309a874f06c90dac73fa0db5
+https://conda.anaconda.org/conda-forge/noarch/jupyter_server-2.14.1-pyhd8ed1ab_0.conda#174af03c6e6038edd32021a48aa003c4
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.16.4-hd8ed1ab_1.conda#37cec2cf68f4c09563d8bc833791096b
+https://conda.anaconda.org/conda-forge/noarch/jupyter-lsp-2.2.5-pyhd8ed1ab_0.conda#885867f6adab3d7ecdf8ab6ca0785f51
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.27.2-pyhd8ed1ab_0.conda#d1cb7b113daaadd89e5aa6a32b28bf0d
+https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.16.4-hd8ed1ab_1.conda#ab83e3b9ca2b111d8f332e9dc8b2170f
+https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.4-pyhd8ed1ab_0.conda#3d85618e2c97ab896b5b5e298d32b5b3
+https://conda.anaconda.org/conda-forge/noarch/jupyterlab-4.2.2-pyhd8ed1ab_0.conda#405a9d330af26391c8001d56b3ef4239
+https://conda.anaconda.org/conda-forge/noarch/nbclassic-1.1.0-pyhd8ed1ab_0.conda#6275b55edf34cfa1f01ba40b699dd915
+https://conda.anaconda.org/conda-forge/noarch/notebook-7.2.1-pyhd8ed1ab_0.conda#08fa71a038c2cac2e636a5a456df15d5
+https://conda.anaconda.org/conda-forge/noarch/widgetsnbextension-3.6.6-pyhd8ed1ab_0.conda#fe79dfe7d51794d665ec3c2fdd4e47c3
+https://conda.anaconda.org/conda-forge/noarch/ipywidgets-7.8.0-pyhd8ed1ab_0.conda#518b05adab6cfe6ea249319932d9d4a3
+https://conda.anaconda.org/conda-forge/noarch/qgrid-1.3.1-pyhd8ed1ab_4.tar.bz2#fff68c7404813a1eb2678425f00e9917
+https://conda.anaconda.org/conda-forge/noarch/nbsphinx-0.9.4-pyhd8ed1ab_0.conda#9dc80eaeff56fb67dbf4f871b81bc13a
+https://conda.anaconda.org/conda-forge/noarch/numpydoc-1.7.0-pyhd8ed1ab_1.conda#66798cbfdcb003d9fbccd92cd08eb3ac
+https://conda.anaconda.org/conda-forge/noarch/recommonmark-0.7.1-pyhd8ed1ab_0.tar.bz2#b3becf9905b8c7ba839072f65e693253
+https://conda.anaconda.org/conda-forge/noarch/sphinx-automodapi-0.17.0-pyh717bed2_1.conda#ee327fec39b9a01d03d3010463df3ee1
+https://conda.anaconda.org/conda-forge/noarch/sphinx-gallery-0.16.0-pyhd8ed1ab_0.conda#add28691ee89e875b190eda07929d5d4
+https://conda.anaconda.org/conda-forge/noarch/sphinx-jsonschema-1.19.1-pyhd8ed1ab_0.tar.bz2#d340bddca07283d3362b0e46b1791568
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-applehelp-1.0.8-pyhd8ed1ab_0.conda#611a35a27914fac3aa37611a6fe40bb5
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-bibtex-2.6.2-pyhd8ed1ab_0.conda#ac0947374ec8b703181808828bf5dfec
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-devhelp-1.0.6-pyhd8ed1ab_0.conda#d7e4954df0d3aea2eacc7835ad12671d
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-htmlhelp-2.0.5-pyhd8ed1ab_0.conda#7e1e7437273682ada2ed5e9e9714b140
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-jquery-4.1-pyhd8ed1ab_0.conda#914897066d5873acfb13e75705276ad1
+https://conda.anaconda.org/conda-forge/noarch/sphinx-astropy-1.9.1-pyhd8ed1ab_0.conda#b6a0939e7b6b3a854b8c8f04606da1a7
+https://conda.anaconda.org/conda-forge/noarch/sphinx_rtd_theme-2.0.0-pyha770c72_0.conda#baf6d9a33df1a789ca55e3b404c7ea28
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-qthelp-1.0.7-pyhd8ed1ab_0.conda#26acae54b06f178681bfb551760f5dd1
+https://conda.anaconda.org/conda-forge/noarch/sphinx-7.3.7-pyhd8ed1ab_0.conda#7b1465205e28d75d2c0e1a868ee00a67
+https://conda.anaconda.org/conda-forge/noarch/sphinxcontrib-serializinghtml-1.1.10-pyhd8ed1ab_0.conda#e507335cb4ca9cff4c3d0fa9cdab255e

From c55122012beba779cab34b5e3ca6849409351c8b Mon Sep 17 00:00:00 2001
From: Andrew <andrewgfullard@gmail.com>
Date: Thu, 11 Jul 2024 23:45:31 -0400
Subject: [PATCH 3/5] Adds continuum marker to pytest and continuum tests
 (#2696)

* Adds continuum marker to pytest and continuum tests

Also applies to tests action, splitting it by marker.

Co-authored-by: Joshua Shields <jvshields@users.noreply.github.com>

* Fix pytest argument

* Update pyproject.toml with correct setting

---------

Co-authored-by: Joshua Shields <jvshields@users.noreply.github.com>
---
 .github/workflows/tests.yml                              | 9 +++++++--
 pyproject.toml                                           | 4 ++++
 .../estimators/tests/test_continuum_property_solver.py   | 1 +
 tardis/transport/montecarlo/tests/test_continuum.py      | 1 +
 4 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 5e12f9ebbdb..640b5f75652 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -22,7 +22,7 @@ on:
 env:
   CACHE_NUMBER: 0  # increase to reset cache manually
   PYTEST_FLAGS: --tardis-refdata=${{ github.workspace }}/tardis-refdata --tardis-regression-data=${{ github.workspace }}/tardis-regression-data
-                --cov=tardis --cov-report=xml --cov-report=html 
+                --cov=tardis --cov-report=xml --cov-report=html
   CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
 concurrency:
@@ -100,7 +100,12 @@ jobs:
           echo "TARDIS_PIP_PATH=$directory_path" >> $GITHUB_ENV
 
       - name: Run tests
-        run: pytest tardis ${{ env.PYTEST_FLAGS }}
+        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m "not continuum"
+        working-directory: ${{ env.TARDIS_PIP_PATH }}
+        if: always()
+
+      - name: Run continuum tests
+        run: pytest tardis ${{ env.PYTEST_FLAGS }} -m continuum
         working-directory: ${{ env.TARDIS_PIP_PATH }}
         if: always()
 
diff --git a/pyproject.toml b/pyproject.toml
index e54125cde14..d2d9c0a5e6f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -186,6 +186,10 @@ tardis_visualization = ["tools/tests/data/*"]
 testpaths = ["tardis"]
 astropy_header = true
 text_file_format = "rst"
+markers = [
+    # continuum tests
+    "continuum",
+]
 
 [tool.tardis]
 edit_on_github = false
\ No newline at end of file
diff --git a/tardis/transport/montecarlo/estimators/tests/test_continuum_property_solver.py b/tardis/transport/montecarlo/estimators/tests/test_continuum_property_solver.py
index 744683a49e9..b3e322c2aa2 100644
--- a/tardis/transport/montecarlo/estimators/tests/test_continuum_property_solver.py
+++ b/tardis/transport/montecarlo/estimators/tests/test_continuum_property_solver.py
@@ -11,6 +11,7 @@
 from tardis.simulation import Simulation
 
 
+@pytest.mark.continuum
 def test_continuum_estimators(
     continuum_config,
     nlte_atomic_dataset,
diff --git a/tardis/transport/montecarlo/tests/test_continuum.py b/tardis/transport/montecarlo/tests/test_continuum.py
index d11b394b2cf..67e448b72a2 100644
--- a/tardis/transport/montecarlo/tests/test_continuum.py
+++ b/tardis/transport/montecarlo/tests/test_continuum.py
@@ -6,6 +6,7 @@
 from tardis.simulation import Simulation
 
 
+@pytest.mark.continuum
 def test_montecarlo_continuum(
     continuum_config,
     regression_data,

From 5d22754e705b98fd96fb22b4f995fb55bba59bce Mon Sep 17 00:00:00 2001
From: Atharva Arya <55894364+atharva-2001@users.noreply.github.com>
Date: Fri, 12 Jul 2024 18:37:59 +0530
Subject: [PATCH 4/5] Move setup environment steps to composite action (#2698)

* Test moving setup environment steps to composite action file

* Replace steps with action in other docs pre release and update refdata
---
 .github/actions/setup_env/action.yml | 32 ++++++++++++++++++++++++++++
 .github/workflows/build-docs.yml     | 20 +++++------------
 .github/workflows/pre-release.yml    | 21 ++++--------------
 .github/workflows/tests.yml          | 22 ++++---------------
 .github/workflows/update-refdata.yml | 21 ++++--------------
 5 files changed, 49 insertions(+), 67 deletions(-)
 create mode 100644 .github/actions/setup_env/action.yml

diff --git a/.github/actions/setup_env/action.yml b/.github/actions/setup_env/action.yml
new file mode 100644
index 00000000000..8c64f24dff4
--- /dev/null
+++ b/.github/actions/setup_env/action.yml
@@ -0,0 +1,32 @@
+name: "Setup environment"
+description: "Sets up environment for tardis and caches it"
+
+inputs:
+  os-label:
+    description: "os label for lock file, default linux"
+    required: true
+    default: "linux"
+
+runs:
+  using: "composite"
+  steps:
+      - name: Download Lock File
+        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-${{ inputs.os-label }}.lock
+        if: matrix.pip == true
+        shell: bash
+      
+      - name: Generate Cache Key
+        run: | 
+          file_hash=$(cat conda-${{ inputs.os-label }}.lock | shasum -a 256 | cut -d' ' -f1)
+          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
+        id: cache-environment-key
+        shell: bash
+        
+      - uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: conda-${{ inputs.os-label }}.lock
+          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
+          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
+          environment-name: tardis
+          cache-environment: true
+          cache-downloads: true
diff --git a/.github/workflows/build-docs.yml b/.github/workflows/build-docs.yml
index 7fc44e742e2..1e5f1ed9a77 100644
--- a/.github/workflows/build-docs.yml
+++ b/.github/workflows/build-docs.yml
@@ -88,28 +88,18 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
         if: github.event_name == 'pull_request_target'
 
-      - name: Generate Cache Key
-        run: |
-          file_hash=$(cat conda-linux-64.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-
       - name: Setup LFS
         uses: ./.github/actions/setup_lfs
+      
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with: 
+          os-label: linux-64
 
       - name: Copy atom_data
         run: |
           mkdir -p ~/Downloads/tardis-data && cp -a ./tardis-refdata/atom_data/. ~/Downloads/tardis-data
 
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda-linux-64.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
-
       - name: Install package
         run: pip install -e .
 
diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
index 69268254ed0..4c3496b428b 100644
--- a/.github/workflows/pre-release.yml
+++ b/.github/workflows/pre-release.yml
@@ -27,23 +27,10 @@ jobs:
         env:
           KEY_SECRET_JSON: ${{ secrets.ZENODO_KEY_SECRET_JSON }}
 
-      - name: Download Lock File
-        run: wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
-
-      - name: Generate Cache Key
-        run: |
-          file_hash=$(cat conda-linux-64.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda-linux-64.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with: 
+          os-label: linux-64
 
       - name: Run Notebook
         run: jupyter nbconvert gather_data.ipynb --to html --execute --ExecutePreprocessor.timeout=6000
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 640b5f75652..dab7e450cdf 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -56,25 +56,11 @@ jobs:
 
       - name: Setup LFS
         uses: ./.github/actions/setup_lfs
-
-      - name: Download Lock File
-        run:  wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-${{ matrix.label }}.lock
-        if: matrix.pip == true
       
-      - name: Generate Cache Key
-        run: | 
-          file_hash=$(cat conda-${{ matrix.label }}.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-        
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda-${{ matrix.label }}.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with: 
+          os-label: ${{ matrix.label }}
 
       - name: Install package editable
         run: |
diff --git a/.github/workflows/update-refdata.yml b/.github/workflows/update-refdata.yml
index 467c2c300e6..6b9f1485c94 100644
--- a/.github/workflows/update-refdata.yml
+++ b/.github/workflows/update-refdata.yml
@@ -32,23 +32,10 @@ jobs:
       - name: Setup LFS
         uses: ./.github/actions/setup_lfs
 
-      - name: Download Lock File
-        run: wget -q https://raw.githubusercontent.com/tardis-sn/tardis/master/conda-linux-64.lock
-
-      - name: Generate Cache Key
-        run: |
-          file_hash=$(cat conda-linux-64.lock | shasum -a 256 | cut -d' ' -f1)
-          echo "file_hash=$file_hash" >> "${GITHUB_OUTPUT}"
-        id: cache-environment-key
-
-      - uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: conda-linux-64.lock
-          cache-environment-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          cache-downloads-key: ${{ steps.cache-environment-key.outputs.file_hash }}
-          environment-name: tardis
-          cache-environment: true
-          cache-downloads: true
+      - name: Setup environment
+        uses: ./.github/actions/setup_env
+        with: 
+          os-label: linux-64
 
       - name: Install package
         run: pip install -e .

From 17b1da429ee99c98fd3ae3f140ab7378be769223 Mon Sep 17 00:00:00 2001
From: Asish Kumar <87874775+officialasishkumar@users.noreply.github.com>
Date: Fri, 12 Jul 2024 19:48:45 +0530
Subject: [PATCH 5/5] Refactor and add more benchmarks for montecarlo (#2640)

* benchmark for energy input package

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor benchmark - remove assert

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* remove energy input source

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* intensity_black_body and test_reverse_binary_search function benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add name and email in .mailmap

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* fix import error of Configuration

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor transport_montecarlo_packet.py

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor transport_montecarlo_numba_formal_integral_p.py

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add FormalIntegrator benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add calculate_spectrum benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add make_source_function and generate_numba_objects in benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add formal_integral from FormalIntegrator class benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add trace_vpacket_volley benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add single_packet_loop benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor vpacket benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor r_packet benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* add montecarlo_main_loop benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor VPacketCollection_add_packet benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor transport_montecarlo_packet.py

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* refactor numba_formal_integral benchmark

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* fix benchmark_base path bug

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* migrate calculate distance functions to a new file

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* bug fix benchmarking

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* removed duplicate function

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* skip benchmark with GNU error

* benchmark single packet loop

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* fix benchmark trace_vpacket_volley

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* fix benchmark single_packet_loop

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* change docstring

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

* fix benchmark formal_integral functions

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>

---------

Signed-off-by: Asish Kumar <officialasishkumar@gmail.com>
---
 .mailmap                                      |   1 +
 benchmarks/benchmark_base.py                  |  84 ++++++++--
 benchmarks/run_tardis.py                      |  10 +-
 .../transport_geometry_calculate_distances.py |  68 ++++++++
 .../transport_montecarlo_interaction.py       |  19 +--
 benchmarks/transport_montecarlo_main_loop.py  |  27 +++
 ...port_montecarlo_numba_formal_integral_p.py | 154 +++++++-----------
 .../transport_montecarlo_numba_interface.py   |  62 +------
 benchmarks/transport_montecarlo_packet.py     | 129 +--------------
 benchmarks/transport_montecarlo_r_packet.py   |  49 +-----
 ...transport_montecarlo_single_packet_loop.py |  26 +++
 benchmarks/transport_montecarlo_vpacket.py    |  54 ++++--
 12 files changed, 305 insertions(+), 378 deletions(-)
 create mode 100644 benchmarks/transport_geometry_calculate_distances.py
 create mode 100644 benchmarks/transport_montecarlo_main_loop.py
 create mode 100644 benchmarks/transport_montecarlo_single_packet_loop.py

diff --git a/.mailmap b/.mailmap
index 3e2a1656bff..b4ed2a7fcbf 100644
--- a/.mailmap
+++ b/.mailmap
@@ -14,6 +14,7 @@ Alice Harpole <aliceharpole@gmail.com>
 Alice Harpole <aliceharpole@gmail.com> Alice Harpole <harpolea@users.noreply.github.com>
 
 Aman Kumar <ak584584@gmail.com>
+Asish Kumar <officialasishkumar@gmail.com>
 
 Andreas Flörs <afloers@mpa-garching.mpg.de>
 Andreas Flörs <afloers@mpa-garching.mpg.de> Andreas Flörs <33418619+afloers@users.noreply.github.com>
diff --git a/benchmarks/benchmark_base.py b/benchmarks/benchmark_base.py
index 3069ce6a1b3..4136fd8b6eb 100644
--- a/benchmarks/benchmark_base.py
+++ b/benchmarks/benchmark_base.py
@@ -5,25 +5,26 @@
 
 import astropy.units as u
 import numpy as np
-import pandas as pd
 from numba import njit
 
 from benchmarks.util.nlte import NLTE
+from tardis import run_tardis
 from tardis.io.atom_data import AtomData
 from tardis.io.configuration import config_reader
 from tardis.io.configuration.config_reader import Configuration
 from tardis.io.util import YAMLLoader, yaml_load_file
 from tardis.model import SimulationState
+from tardis.model.geometry.radial1d import NumbaRadial1DGeometry
 from tardis.simulation import Simulation
 from tardis.tests.fixtures.atom_data import DEFAULT_ATOM_DATA_UUID
 from tardis.tests.fixtures.regression_data import RegressionData
-from tardis.transport.montecarlo import RPacket
-from tardis.transport.montecarlo.numba_interface import (
-    opacity_state_initialize,
-)
+from tardis.transport.montecarlo import RPacket, montecarlo_configuration
+from tardis.transport.montecarlo.estimators import radfield_mc_estimators
+from tardis.transport.montecarlo.numba_interface import opacity_state_initialize
 from tardis.transport.montecarlo.packet_collections import (
     VPacketCollection,
 )
+from tardis.transport.montecarlo.packet_trackers import RPacketTracker
 
 
 class BenchmarkBase:
@@ -350,13 +351,66 @@ def generate_reference(self):
             return option
 
     @property
-    def tardis_ref_data(self):
-        # TODO: This function is not working in the benchmarks.
-        if self.generate_reference:
-            mode = "w"
-        else:
-            mode = "r"
-        with pd.HDFStore(
-            f"{self.tardis_ref_path}/unit_test_data.h5", mode=mode
-        ) as store:
-            yield store
+    def verysimple_radfield_mc_estimators(self):
+        plasma = self.nb_simulation_verysimple.plasma
+        return radfield_mc_estimators.initialize_estimator_statistics(
+            plasma.tau_sobolevs.shape, plasma.gamma.shape
+        )
+
+    @property
+    def montecarlo_configuration(self):
+        return montecarlo_configuration.MonteCarloConfiguration()
+
+    @property
+    def rpacket_tracker(self): 
+        return RPacketTracker(0)
+
+    @property
+    def transport_state(self):
+        return self.nb_simulation_verysimple.transport.transport_state
+
+    @property
+    def simulation_rpacket_tracking_enabled(self):
+        config_verysimple = self.config_verysimple
+        config_verysimple.montecarlo.iterations = 3
+        config_verysimple.montecarlo.no_of_packets = 4000
+        config_verysimple.montecarlo.last_no_of_packets = -1
+        config_verysimple.spectrum.virtual.virtual_packet_logging = True
+        config_verysimple.montecarlo.no_of_virtual_packets = 1
+        config_verysimple.montecarlo.tracking.track_rpacket = True
+        config_verysimple.spectrum.num = 2000
+        atomic_data = deepcopy(self.atomic_dataset)
+        sim = run_tardis(
+            config_verysimple,
+            atom_data=atomic_data,
+            show_convergence_plots=False,
+        )
+        return sim
+
+    @property
+    def geometry(self):
+        return NumbaRadial1DGeometry(
+            r_inner=np.array([6.912e14, 8.64e14], dtype=np.float64),
+            r_outer=np.array([8.64e14, 1.0368e15], dtype=np.float64),
+            v_inner=np.array([-1, -1], dtype=np.float64),
+            v_outer=np.array([-1, -1], dtype=np.float64),
+        )
+
+
+    @property
+    def estimators(self):
+        return radfield_mc_estimators.RadiationFieldMCEstimators(
+            j_estimator=np.array([0.0, 0.0], dtype=np.float64),
+            nu_bar_estimator=np.array([0.0, 0.0], dtype=np.float64),
+            j_blue_estimator=np.array(
+                [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]], dtype=np.float64
+            ),
+            Edotlu_estimator=np.array(
+                [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0]], dtype=np.float64
+            ),
+            photo_ion_estimator=np.empty((0, 0), dtype=np.float64),
+            stim_recomb_estimator=np.empty((0, 0), dtype=np.float64),
+            bf_heating_estimator=np.empty((0, 0), dtype=np.float64),
+            stim_recomb_cooling_estimator=np.empty((0, 0), dtype=np.float64),
+            photo_ion_estimator_statistics=np.empty((0, 0), dtype=np.int64),
+        )
diff --git a/benchmarks/run_tardis.py b/benchmarks/run_tardis.py
index 8fca11f6030..6fcb2f7d244 100644
--- a/benchmarks/run_tardis.py
+++ b/benchmarks/run_tardis.py
@@ -4,8 +4,6 @@
 
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis import run_tardis
-from tardis.io.configuration.config_reader import Configuration
-
 
 class BenchmarkRunTardis(BenchmarkBase):
     """
@@ -14,12 +12,8 @@ class BenchmarkRunTardis(BenchmarkBase):
 
     def __init__(self):
         super().__init__()
-        self.config = None
-
-    def setup(self):
         filename = "data/tardis_configv1_benchmark.yml"
-        path = self.get_relative_path(filename)
-        self.config = Configuration.from_yaml(path)
+        self.path = self.get_relative_path(filename)
 
     def time_run_tardis(self):
-        run_tardis(self.config, log_level="ERROR", show_progress_bars=False)
+        run_tardis(self.path, log_level="ERROR", show_progress_bars=False)
diff --git a/benchmarks/transport_geometry_calculate_distances.py b/benchmarks/transport_geometry_calculate_distances.py
new file mode 100644
index 00000000000..4f5829f40b8
--- /dev/null
+++ b/benchmarks/transport_geometry_calculate_distances.py
@@ -0,0 +1,68 @@
+from asv_runner.benchmarks.mark import parameterize
+
+import tardis.transport.frame_transformations as frame_transformations
+import tardis.transport.geometry.calculate_distances as calculate_distances
+from benchmarks.benchmark_base import BenchmarkBase
+
+
+class BenchmarkTransportGeometryCalculateDistances(BenchmarkBase):
+    """
+    Class to benchmark the calculate distances function.
+    """
+
+    @property
+    def model(self):
+        return 5.2e7
+
+    def time_calculate_distance_boundary(self):
+        mu = 0.3
+        r = 7.5e14
+
+        calculate_distances.calculate_distance_boundary(
+            r, mu, self.geometry.r_inner[0], self.geometry.r_outer[0]
+        )
+
+    @parameterize(
+        {
+            "Parameters": [
+                {
+                    "packet": {
+                        "nu_line": 0.1,
+                        "is_last_line": True
+                    },
+                    "enable_full_relativity": True,
+                },
+                {
+                    "packet": {
+                        "nu_line": 0.2,
+                        "is_last_line": False
+                    },
+                    "enable_full_relativity": True,
+                }
+            ]
+        }
+    )
+    def time_calculate_distance_line(self, parameters):
+        packet_params = parameters["packet"]
+        nu_line = packet_params["nu_line"]
+        is_last_line = packet_params["is_last_line"]
+        enable_full_relativity = parameters["enable_full_relativity"]
+
+        time_explosion = self.model
+
+        doppler_factor = frame_transformations.get_doppler_factor(
+            self.static_packet.r,
+            self.static_packet.mu,
+            time_explosion,
+            enable_full_relativity
+        )
+        comov_nu = self.static_packet.nu * doppler_factor
+
+        calculate_distances.calculate_distance_line(
+            self.static_packet,
+            comov_nu,
+            is_last_line,
+            nu_line,
+            time_explosion,
+            enable_full_relativity
+        )
diff --git a/benchmarks/transport_montecarlo_interaction.py b/benchmarks/transport_montecarlo_interaction.py
index b27d3ac9396..12fb8789830 100644
--- a/benchmarks/transport_montecarlo_interaction.py
+++ b/benchmarks/transport_montecarlo_interaction.py
@@ -2,17 +2,15 @@
 Basic TARDIS Benchmark.
 """
 
-import numpy as np
-from asv_runner.benchmarks.mark import parameterize, skip_benchmark
-
 import tardis.transport.montecarlo.interaction as interaction
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis.transport.montecarlo.numba_interface import (
     LineInteractionType,
 )
+from asv_runner.benchmarks.mark import parameterize
+
 
 
-@skip_benchmark
 class BenchmarkMontecarloMontecarloNumbaInteraction(BenchmarkBase):
     """
     Class to benchmark the numba interaction function.
@@ -30,10 +28,6 @@ def time_thomson_scatter(self):
             packet, time_explosion, enable_full_relativity
         )
 
-        assert np.abs(packet.mu - init_mu) > 1e-7
-        assert np.abs(packet.nu - init_nu) > 1e-7
-        assert np.abs(packet.energy - init_energy) > 1e-7
-
     @parameterize(
         {
             "Line interaction type": [
@@ -45,9 +39,6 @@ def time_thomson_scatter(self):
     )
     def time_line_scatter(self, line_interaction_type):
         packet = self.packet
-        init_mu = packet.mu
-        init_nu = packet.nu
-        init_energy = packet.energy
         packet.initialize_line_id(
             self.verysimple_opacity_state,
             self.verysimple_time_explosion,
@@ -64,10 +55,6 @@ def time_line_scatter(self, line_interaction_type):
             self.verysimple_continuum_processes_enabled,
         )
 
-        assert np.abs(packet.mu - init_mu) > 1e-7
-        assert np.abs(packet.nu - init_nu) > 1e-7
-        assert np.abs(packet.energy - init_energy) > 1e-7
-
     @parameterize(
         {
             "Test packet": [
@@ -109,5 +96,3 @@ def time_line_emission(self, test_packet):
             self.verysimple_opacity_state,
             self.verysimple_enable_full_relativity,
         )
-
-        assert packet.next_line_id == emission_line_id + 1
diff --git a/benchmarks/transport_montecarlo_main_loop.py b/benchmarks/transport_montecarlo_main_loop.py
new file mode 100644
index 00000000000..7b91d0867c1
--- /dev/null
+++ b/benchmarks/transport_montecarlo_main_loop.py
@@ -0,0 +1,27 @@
+"""
+Basic TARDIS Benchmark.
+"""
+
+from benchmarks.benchmark_base import BenchmarkBase
+from tardis.transport.montecarlo.montecarlo_main_loop import montecarlo_main_loop
+
+
+class BenchmarkTransportMontecarloMainLoop(BenchmarkBase):
+    """
+    class to benchmark montecarlo_main_loop function.
+    """
+
+    def time_montecarlo_main_loop(self):
+        montecarlo_main_loop(
+            self.transport_state.packet_collection,
+            self.transport_state.geometry_state,
+            self.verysimple_time_explosion,
+            self.transport_state.opacity_state,
+            self.montecarlo_configuration,
+            self.transport_state.radfield_mc_estimators,
+            self.transport_state.spectrum_frequency.value,
+            self.montecarlo_configuration.NUMBER_OF_VPACKETS,
+            iteration=0,
+            show_progress_bars=False,
+            total_iterations=0
+        )
diff --git a/benchmarks/transport_montecarlo_numba_formal_integral_p.py b/benchmarks/transport_montecarlo_numba_formal_integral_p.py
index 0e084505404..8c772d2c0cc 100644
--- a/benchmarks/transport_montecarlo_numba_formal_integral_p.py
+++ b/benchmarks/transport_montecarlo_numba_formal_integral_p.py
@@ -3,41 +3,68 @@
 """
 
 import numpy as np
-from asv_runner.benchmarks.mark import parameterize, skip_benchmark
+from asv_runner.benchmarks.mark import parameterize
+from numba import config
 
 import tardis.transport.montecarlo.formal_integral as formal_integral
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis import constants as c
+from tardis import run_tardis
+from tardis.io.configuration.config_reader import Configuration
 from tardis.model.geometry.radial1d import NumbaRadial1DGeometry
-from tardis.util.base import intensity_black_body
 
+config.THREADING_LAYER='workqueue'
 
 class BenchmarkMontecarloMontecarloNumbaNumbaFormalIntegral(BenchmarkBase):
     """
     Class to benchmark the numba formal integral function.
     """
 
+    def __init__(self):
+        super().__init__()
+
+        self.config = None
+        filename = "data/tardis_configv1_benchmark.yml"
+        path = self.get_relative_path(filename)
+        self.config = Configuration.from_yaml(path)
+
+        self.Simulation = run_tardis(
+            self.config, log_level="ERROR", show_progress_bars=False
+        )
+
+        self.FormalIntegrator = formal_integral.FormalIntegrator(
+            self.Simulation.simulation_state, self.Simulation.plasma, self.Simulation.transport
+        )
+
     @parameterize(
         {
-            "nu": [1e14, 0, 1],
-            "temperature": [1e4, 1, 1],
+            "Parameters": [
+                {
+                    "nu": 1e14,
+                    "temperature": 1e4,
+                },
+                {
+                    "nu": 0,
+                    "temperature": 1,
+                },
+                {
+                    "nu": 1,
+                    "temperature": 1,
+                }
+            ]
         }
     )
-    def time_intensity_black_body(self, nu, temperature):
-        func = formal_integral.intensity_black_body
-        actual = func(nu, temperature)
-        print(actual, type(actual))
-        intensity_black_body(nu, temperature)
+    def time_intensity_black_body(self, parameters):
+        nu = parameters["nu"]
+        temperature = parameters["temperature"]
+        formal_integral.intensity_black_body(nu, temperature)
 
     @parameterize({"N": (1e2, 1e3, 1e4, 1e5)})
     def time_trapezoid_integration(self, n):
-        func = formal_integral.trapezoid_integration
         h = 1.0
-        n = int(n)
-        data = np.random.random(n)
+        data = np.random.random(int(n))
 
-        func(data, h)
-        np.trapz(data)
+        formal_integral.trapezoid_integration(data, h)
 
     @staticmethod
     def calculate_z(r, p):
@@ -83,94 +110,25 @@ def time_explosion(self):
 
     @parameterize({"p": [0.0, 0.5, 1.0], "Test data": TESTDATA})
     def time_calculate_z(self, p, test_data):
-        func = formal_integral.calculate_z
-        inv_t = 1.0 / self.time_explosion
-        len(self.formal_integral_geometry(test_data).r_outer)
+        inv_t = 1.0 / self.verysimple_time_explosion
         r_outer = self.formal_integral_geometry(test_data).r_outer
 
         for r in r_outer:
-            actual = func(r, p, inv_t)
-            if p >= r:
-                assert actual == 0
-            else:
-                np.sqrt(r * r - p * p) * formal_integral.C_INV * inv_t
-
-    @skip_benchmark
-    @parameterize({"p": [0, 0.5, 1], "Test data": TESTDATA})
-    def time_populate_z_photosphere(self, p, test_data):
-        formal_integral.FormalIntegrator(
-            self.formal_integral_geometry(test_data), None, None
-        )
-        func = formal_integral.populate_z
-        size = len(self.formal_integral_geometry(test_data).r_outer)
-        r_inner = self.formal_integral_geometry(test_data).r_inner
-        self.formal_integral_geometry(test_data).r_outer
-
-        p = r_inner[0] * p
-        oz = np.zeros_like(r_inner)
-        oshell_id = np.zeros_like(oz, dtype=np.int64)
-
-        n = func(
-            self.formal_integral_geometry(test_data),
-            self.formal_integral_geometry(test_data),
-            p,
-            oz,
-            oshell_id,
-        )
-        assert n == size
-
-    @skip_benchmark
-    @parameterize({"p": [1e-5, 0.5, 0.99, 1], "Test data": TESTDATA})
-    def time_populate_z_shells(self, p, test_data):
-        formal_integral.FormalIntegrator(
-            self.formal_integral_geometry(test_data), None, None
-        )
-        func = formal_integral.populate_z
-
-        size = len(self.formal_integral_geometry(test_data).r_inner)
-        r_inner = self.formal_integral_geometry(test_data).r_inner
-        r_outer = self.formal_integral_geometry(test_data).r_outer
-
-        p = r_inner[0] + (r_outer[-1] - r_inner[0]) * p
-        idx = np.searchsorted(r_outer, p, side="right")
-
-        oz = np.zeros(size * 2)
-        oshell_id = np.zeros_like(oz, dtype=np.int64)
-
-        offset = size - idx
-
-        expected_n = (offset) * 2
-        expected_oz = np.zeros_like(oz)
-        expected_oshell_id = np.zeros_like(oshell_id)
-
-        # Calculated way to determine which shells get hit
-        expected_oshell_id[:expected_n] = (
-            np.abs(np.arange(0.5, expected_n, 1) - offset) - 0.5 + idx
-        )
-
-        expected_oz[0:offset] = 1 + self.calculate_z(
-            r_outer[np.arange(size, idx, -1) - 1], p
-        )
-        expected_oz[offset:expected_n] = 1 - self.calculate_z(
-            r_outer[np.arange(idx, size, 1)], p
-        )
-
-        n = func(
-            self.formal_integral_geometry(test_data),
-            self.formal_integral_geometry(test_data),
-            p,
-            oz,
-            oshell_id,
-        )
-
-        assert n == expected_n
+            formal_integral.calculate_z(r, p, inv_t)
 
     @parameterize({"N": [100, 1000, 10000]})
-    def time_calculate_p_values(self, n):
+    def time_calculate_p_values(self, N):
         r = 1.0
-        func = formal_integral.calculate_p_values
+        formal_integral.calculate_p_values(r, N)
 
-        expected = r / (n - 1) * np.arange(0, n, dtype=np.float64)
-        np.zeros_like(expected, dtype=np.float64)
-
-        func(r, n)
+    # Benchmark for functions in FormalIntegrator class
+    def time_FormalIntegrator_functions(self):
+        self.FormalIntegrator.calculate_spectrum(
+            self.Simulation.transport.transport_state.spectrum.frequency
+        )
+        self.FormalIntegrator.make_source_function()
+        self.FormalIntegrator.generate_numba_objects()
+        self.FormalIntegrator.formal_integral(
+            self.Simulation.transport.transport_state.spectrum.frequency,
+            1000
+        )
diff --git a/benchmarks/transport_montecarlo_numba_interface.py b/benchmarks/transport_montecarlo_numba_interface.py
index bb9ac4e5b8d..ac8f79791f6 100644
--- a/benchmarks/transport_montecarlo_numba_interface.py
+++ b/benchmarks/transport_montecarlo_numba_interface.py
@@ -5,7 +5,7 @@
 import numpy as np
 from asv_runner.benchmarks.mark import parameterize
 
-import tardis.opacities.opacity_state as numba_interface
+from tardis.opacities.opacity_state import opacity_state_initialize
 from benchmarks.benchmark_base import BenchmarkBase
 
 
@@ -18,65 +18,9 @@ class BenchmarkMontecarloMontecarloNumbaNumbaInterface(BenchmarkBase):
     def time_opacity_state_initialize(self, input_params):
         line_interaction_type = input_params
         plasma = self.nb_simulation_verysimple.plasma
-        numba_interface.opacity_state_initialize(
+        opacity_state_initialize(
             plasma,
             line_interaction_type,
             self.verysimple_disable_line_scattering,
             self.verysimple_continuum_processes_enabled,
-        )
-
-        if line_interaction_type == "scatter":
-            np.zeros(1, dtype=np.int64)
-
-    def time_VPacketCollection_add_packet(self):
-        verysimple_3vpacket_collection = self.verysimple_3vpacket_collection
-        assert verysimple_3vpacket_collection.length == 0
-
-        nus = [3.0e15, 0.0, 1e15, 1e5]
-        energies = [0.4, 0.1, 0.6, 1e10]
-        initial_mus = [0.1, 0, 1, 0.9]
-        initial_rs = [3e42, 4.5e45, 0, 9.0e40]
-        last_interaction_in_nus = np.array(
-            [3.0e15, 0.0, 1e15, 1e5], dtype=np.float64
-        )
-        last_interaction_types = np.array([1, 1, 3, 2], dtype=np.int64)
-        last_interaction_in_ids = np.array([100, 0, 1, 1000], dtype=np.int64)
-        last_interaction_out_ids = np.array(
-            [1201, 123, 545, 1232], dtype=np.int64
-        )
-        last_interaction_shell_ids = np.array([2, -1, 6, 0], dtype=np.int64)
-
-        for (
-            nu,
-            energy,
-            initial_mu,
-            initial_r,
-            last_interaction_in_nu,
-            last_interaction_type,
-            last_interaction_in_id,
-            last_interaction_out_id,
-            last_interaction_shell_id,
-        ) in zip(
-            nus,
-            energies,
-            initial_mus,
-            initial_rs,
-            last_interaction_in_nus,
-            last_interaction_types,
-            last_interaction_in_ids,
-            last_interaction_out_ids,
-            last_interaction_shell_ids,
-        ):
-            verysimple_3vpacket_collection.add_packet(
-                nu,
-                energy,
-                initial_mu,
-                initial_r,
-                last_interaction_in_nu,
-                last_interaction_type,
-                last_interaction_in_id,
-                last_interaction_out_id,
-                last_interaction_shell_id,
-            )
-
-        assert verysimple_3vpacket_collection.length == 9
+        )
\ No newline at end of file
diff --git a/benchmarks/transport_montecarlo_packet.py b/benchmarks/transport_montecarlo_packet.py
index 088cda90d7f..fd9a262a93a 100644
--- a/benchmarks/transport_montecarlo_packet.py
+++ b/benchmarks/transport_montecarlo_packet.py
@@ -2,21 +2,15 @@
 Basic TARDIS Benchmark.
 """
 
-import numpy as np
-from asv_runner.benchmarks.mark import parameterize, skip_benchmark
-
-import tardis.transport.frame_transformations as frame_transformations
+import tardis.opacities.opacities as opacities
 import tardis.transport.geometry.calculate_distances as calculate_distances
-import tardis.transport.montecarlo.estimators.radfield_mc_estimators
-import tardis.transport.montecarlo.opacities as opacities
-import tardis.transport.montecarlo.r_packet as r_packet
 import tardis.transport.montecarlo.r_packet_transport as r_packet_transport
 import tardis.transport.montecarlo.utils as utils
 from benchmarks.benchmark_base import BenchmarkBase
-from tardis.model.geometry.radial1d import NumbaRadial1DGeometry
 from tardis.transport.montecarlo.estimators.radfield_estimator_calcs import (
     update_line_estimators,
 )
+from asv_runner.benchmarks.mark import parameterize
 
 
 class BenchmarkMontecarloMontecarloNumbaPacket(BenchmarkBase):
@@ -24,111 +18,6 @@ class BenchmarkMontecarloMontecarloNumbaPacket(BenchmarkBase):
     Class to benchmark the numba packet function.
     """
 
-    @property
-    def geometry(self):
-        return NumbaRadial1DGeometry(
-            r_inner=np.array([6.912e14, 8.64e14], dtype=np.float64),
-            r_outer=np.array([8.64e14, 1.0368e15], dtype=np.float64),
-            v_inner=np.array([-1, -1], dtype=np.float64),
-            v_outer=np.array([-1, -1], dtype=np.float64),
-        )
-
-    @property
-    def model(self):
-        return 5.2e7
-
-    @property
-    def estimators(self):
-        return tardis.transport.montecarlo.estimators.radfield_mc_estimators.RadiationFieldMCEstimators(
-            j_estimator=np.array([0.0, 0.0], dtype=np.float64),
-            nu_bar_estimator=np.array([0.0, 0.0], dtype=np.float64),
-            j_blue_estimator=np.array(
-                [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]], dtype=np.float64
-            ),
-            Edotlu_estimator=np.array(
-                [[0.0, 0.0, 1.0], [0.0, 0.0, 1.0]], dtype=np.float64
-            ),
-            photo_ion_estimator=np.empty((0, 0), dtype=np.float64),
-            stim_recomb_estimator=np.empty((0, 0), dtype=np.float64),
-            bf_heating_estimator=np.empty((0, 0), dtype=np.float64),
-            stim_recomb_cooling_estimator=np.empty((0, 0), dtype=np.float64),
-            photo_ion_estimator_statistics=np.empty((0, 0), dtype=np.int64),
-        )
-
-    @parameterize(
-        {
-            "Packet params": [
-                {"mu": 0.3, "r": 7.5e14},
-                {"mu": -0.3, "r": 7.5e13},
-                {"mu": -0.3, "r": 7.5e14},
-            ]
-        }
-    )
-    def time_calculate_distance_boundary(self, packet_params):
-        mu = packet_params["mu"]
-        r = packet_params["r"]
-
-        calculate_distances.calculate_distance_boundary(
-            r, mu, self.geometry.r_inner[0], self.geometry.r_outer[0]
-        )
-
-    @parameterize(
-        {
-            "Parameters": [
-                {
-                    "packet": {"nu_line": 0.1, "is_last_line": True},
-                    "expected": None,
-                    "enable_full_relativity": True,
-                },
-                {
-                    "packet": {"nu_line": 0.2, "is_last_line": False},
-                    "expected": None,
-                    "enable_full_relativity": True,
-                },
-                {
-                    "packet": {"nu_line": 0.5, "is_last_line": False},
-                    "expected": utils.MonteCarloException,
-                    "enable_full_relativity": False,
-                },
-                {
-                    "packet": {"nu_line": 0.6, "is_last_line": False},
-                    "expected": utils.MonteCarloException,
-                    "enable_full_relativity": False,
-                },
-            ]
-        }
-    )
-    def time_calculate_distance_line(self, parameters):
-        packet_params = parameters["packet"]
-        expected_params = parameters["expected"]
-        nu_line = packet_params["nu_line"]
-        is_last_line = packet_params["is_last_line"]
-        enable_full_relativity = parameters["enable_full_relativity"]
-
-        time_explosion = self.model
-        doppler_factor = frame_transformations.get_doppler_factor(
-            self.static_packet.r,
-            self.static_packet.mu,
-            time_explosion,
-            enable_full_relativity,
-        )
-        comov_nu = self.static_packet.nu * doppler_factor
-
-        obtained_tardis_error = None
-        try:
-            calculate_distances.calculate_distance_line(
-                self.static_packet,
-                comov_nu,
-                is_last_line,
-                nu_line,
-                time_explosion,
-                enable_full_relativity,
-            )
-        except utils.MonteCarloException:
-            obtained_tardis_error = utils.MonteCarloException
-
-        assert obtained_tardis_error == expected_params
-
     @parameterize(
         {
             "Parameters": [
@@ -136,7 +25,10 @@ def time_calculate_distance_line(self, parameters):
                     "electron_density": 1e-5,
                     "tua_event": 1e10,
                 },
-                {"electron_density": 1.0, "tua_event": 1e10},
+                {
+                    "electron_density": 1.0,
+                    "tua_event": 1e10
+                },
             ]
         }
     )
@@ -175,10 +67,7 @@ def time_calculate_tau_electron(self, parameters):
         opacities.calculate_tau_electron(electron_density, distance)
 
     def time_get_random_mu(self):
-        self.set_seed_fixture(1963)
-
-        output1 = utils.get_random_mu()
-        assert output1 == 0.9136407866175174
+        utils.get_random_mu()
 
     @parameterize(
         {
@@ -248,9 +137,7 @@ def time_move_packet_across_shell_boundary_emitted(self, parameters):
         r_packet_transport.move_packet_across_shell_boundary(
             packet, delta_shell, no_of_shells
         )
-        assert packet.status == r_packet.PacketStatus.EMITTED
 
-    @skip_benchmark
     @parameterize(
         {
             "Parameters": [
@@ -281,7 +168,6 @@ def time_move_packet_across_shell_boundary_reabsorbed(self, parameters):
         r_packet_transport.move_packet_across_shell_boundary(
             packet, delta_shell, no_of_shells
         )
-        assert packet.status == r_packet.PacketStatus.REABSORBED
 
     @parameterize(
         {
@@ -313,4 +199,3 @@ def time_move_packet_across_shell_boundary_increment(self, parameters):
         r_packet_transport.move_packet_across_shell_boundary(
             packet, delta_shell, no_of_shells
         )
-        assert packet.current_shell_id == current_shell_id + delta_shell
diff --git a/benchmarks/transport_montecarlo_r_packet.py b/benchmarks/transport_montecarlo_r_packet.py
index 3ee85eef518..40b7d8bf7e6 100644
--- a/benchmarks/transport_montecarlo_r_packet.py
+++ b/benchmarks/transport_montecarlo_r_packet.py
@@ -1,11 +1,7 @@
 """
 Basic TARDIS Benchmark.
 """
-
-from copy import deepcopy
-
 from benchmarks.benchmark_base import BenchmarkBase
-from tardis.base import run_tardis
 from tardis.transport.montecarlo.packet_trackers import (
     rpacket_trackers_to_dataframe,
 )
@@ -16,52 +12,9 @@ class BenchmarkMontecarloMontecarloNumbaRPacket(BenchmarkBase):
     Class to benchmark the numba R packet function.
     """
 
-    @property
-    def simulation_rpacket_tracking_enabled(self):
-        config_verysimple = self.config_verysimple
-        config_verysimple.montecarlo.iterations = 3
-        config_verysimple.montecarlo.no_of_packets = 4000
-        config_verysimple.montecarlo.last_no_of_packets = -1
-        config_verysimple.spectrum.virtual.virtual_packet_logging = True
-        config_verysimple.montecarlo.no_of_virtual_packets = 1
-        config_verysimple.montecarlo.tracking.track_rpacket = True
-        config_verysimple.spectrum.num = 2000
-        atomic_data = deepcopy(self.atomic_dataset)
-        sim = run_tardis(
-            config_verysimple,
-            atom_data=atomic_data,
-            show_convergence_plots=False,
-        )
-        return sim
-
     def time_rpacket_trackers_to_dataframe(self):
         sim = self.simulation_rpacket_tracking_enabled
         transport_state = sim.transport.transport_state
-        rtracker_df = rpacket_trackers_to_dataframe(
+        rpacket_trackers_to_dataframe(
             transport_state.rpacket_tracker
         )
-
-        # check df shape and column names
-        assert rtracker_df.shape == (
-            sum(
-                [len(tracker.r) for tracker in transport_state.rpacket_tracker]
-            ),
-            8,
-        )
-
-        # check all data with rpacket_tracker
-        expected_rtrackers = []
-        for rpacket in transport_state.rpacket_tracker:
-            for rpacket_step_no in range(len(rpacket.r)):
-                expected_rtrackers.append(
-                    [
-                        rpacket.status[rpacket_step_no],
-                        rpacket.seed,
-                        rpacket.r[rpacket_step_no],
-                        rpacket.nu[rpacket_step_no],
-                        rpacket.mu[rpacket_step_no],
-                        rpacket.energy[rpacket_step_no],
-                        rpacket.shell_id[rpacket_step_no],
-                        rpacket.interaction_type[rpacket_step_no],
-                    ]
-                )
diff --git a/benchmarks/transport_montecarlo_single_packet_loop.py b/benchmarks/transport_montecarlo_single_packet_loop.py
new file mode 100644
index 00000000000..89f3d247354
--- /dev/null
+++ b/benchmarks/transport_montecarlo_single_packet_loop.py
@@ -0,0 +1,26 @@
+"""
+Basic TARDIS Benchmark.
+"""
+
+from benchmarks.benchmark_base import BenchmarkBase
+from tardis.transport.montecarlo import single_packet_loop
+from numba.np.ufunc.parallel import get_num_threads, get_thread_id
+
+
+class BenchmarkMontecarloMontecarloNumbaVpacket(BenchmarkBase):
+    """
+    Class to benchmark the single packet loop function.
+    """
+
+    def time_single_packet_loop(self):
+        single_packet_loop.single_packet_loop(
+            self.packet,
+            self.verysimple_numba_radial_1d_geometry,
+            self.verysimple_time_explosion,
+            self.verysimple_opacity_state,
+            self.transport_state.radfield_mc_estimators.create_estimator_list(get_num_threads())[get_thread_id()],
+            self.verysimple_3vpacket_collection,
+            self.rpacket_tracker,
+            self.montecarlo_configuration
+        )
+
diff --git a/benchmarks/transport_montecarlo_vpacket.py b/benchmarks/transport_montecarlo_vpacket.py
index a1141a89c65..22198150f43 100644
--- a/benchmarks/transport_montecarlo_vpacket.py
+++ b/benchmarks/transport_montecarlo_vpacket.py
@@ -3,8 +3,10 @@
 """
 
 import numpy as np
+from asv_runner.benchmarks.mark import parameterize
 
 import tardis.transport.montecarlo.vpacket as vpacket
+from tardis.transport.montecarlo.r_packet import RPacket
 from benchmarks.benchmark_base import BenchmarkBase
 from tardis.transport.frame_transformations import (
     get_doppler_factor,
@@ -27,6 +29,17 @@ def v_packet(self):
             next_line_id=0,
             index=0,
         )
+    
+    @property
+    def r_packet(self):
+        return RPacket(
+            r=7.5e14,
+            nu=4e18,
+            mu=self.verysimple_packet_collection.initial_mus[0],
+            energy=self.verysimple_packet_collection.initial_energies[0],
+            seed=1963,
+            index=0,
+        )
 
     def v_packet_initialize_line_id(
         self, v_packet, opacity_state, time_explosion, enable_full_relativity
@@ -61,11 +74,7 @@ def time_trace_vpacket_within_shell(self):
             enable_full_relativity,
         )
 
-        (
-            tau_trace_combined,
-            distance_boundary,
-            delta_shell,
-        ) = vpacket.trace_vpacket_within_shell(
+        vpacket.trace_vpacket_within_shell(
             v_packet,
             verysimple_numba_radial_1d_geometry,
             verysimple_time_explosion,
@@ -74,8 +83,6 @@ def time_trace_vpacket_within_shell(self):
             continuum_processes_enabled,
         )
 
-        assert delta_shell == 1
-
     def time_trace_vpacket(self):
         v_packet = self.v_packet
         verysimple_numba_radial_1d_geometry = (
@@ -101,7 +108,7 @@ def time_trace_vpacket(self):
             enable_full_relativity,
         )
 
-        tau_trace_combined = vpacket.trace_vpacket(
+        vpacket.trace_vpacket(
             v_packet,
             verysimple_numba_radial_1d_geometry,
             verysimple_time_explosion,
@@ -112,9 +119,6 @@ def time_trace_vpacket(self):
             continuum_processes_enabled,
         )
 
-        assert v_packet.next_line_id == 2773
-        assert v_packet.current_shell_id == 1
-
     @property
     def broken_packet(self):
         return vpacket.VPacket(
@@ -151,3 +155,31 @@ def time_trace_bad_vpacket(self):
             enable_full_relativity,
             continuum_processes_enabled,
         )
+
+    @parameterize(
+        {
+            "Paramters": [
+                {
+                    "tau_russian": 10.0,
+                    "survival_possibility": 0.0
+                },
+                {
+                    "tau_russian": 15.0,
+                    "survival_possibility": 0.1
+                },
+            ]
+        }
+    )
+    def time_trace_vpacket_volley(self, parameters):
+        vpacket.trace_vpacket_volley(
+            self.r_packet,
+            self.verysimple_3vpacket_collection,
+            self.verysimple_numba_radial_1d_geometry,
+            self.verysimple_time_explosion,
+            self.verysimple_opacity_state,
+            False,
+            parameters["tau_russian"],
+            parameters["survival_possibility"],
+            False
+        )
+