From 503da2c9918c199b7eb50127f0b778656dc7d178 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 11:01:00 +0200 Subject: [PATCH 01/69] adding files --- recipes/pyscenic/build.sh | 31 ++++++++++++++++ recipes/pyscenic/meta.yaml | 73 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 104 insertions(+) create mode 100644 recipes/pyscenic/build.sh create mode 100644 recipes/pyscenic/meta.yaml diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh new file mode 100644 index 0000000000000..ff07df22a6eea --- /dev/null +++ b/recipes/pyscenic/build.sh @@ -0,0 +1,31 @@ +#!/bin/bash +set -ex + +if [ -z "${PYTHON}" ]; then + PYTHON=$(which python) +fi + + +pushd ${SRC_DIR}/pyscenic-0.12.1 +${PYTHON} -m pip install . --no-deps --ignore-installed -vv +popd + +for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0 +do + pushd ${SRC_DIR}/${package} + + if [ "$package" == "arboreto-0.1.6" ]; then + if [ ! -f requirements.txt ]; then + echo "Creating requirements.txt for arboreto" + echo "dask[complete]" > requirements.txt + echo "distributed" >> requirements.txt + echo "numpy>=1.16.5" >> requirements.txt + echo "pandas" >> requirements.txt + echo "scikit-learn" >> requirements.txt + echo "scipy" >> requirements.txt + fi + fi + + ${PYTHON} -m pip install --use-pep517 -vv --no-deps . + popd +done diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml new file mode 100644 index 0000000000000..7a25e71929684 --- /dev/null +++ b/recipes/pyscenic/meta.yaml @@ -0,0 +1,73 @@ +{% set name = "pyscenic" %} +{% set version = "0.12.1" %} +{% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + - url: https://pypi.io/packages/source/p/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} + folder: pyscenic-0.12.1 + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} + +requirements: + host: + - python=3.10 + - pip + - setuptools_scm + - dask[complete] + - distributed + - numpy >=1.16.5 + - pandas + - scikit-learn + - scipy + - {{ compiler('c') }} + run: + - python=3.10 + - aiohttp + - frozendict + - numpy >=1.19 + - pandas >=1.3 + - scipy >=1.6 + - llvmlite >=0.34 + - numba >=0.51.2 + - click >=7.0 + - cloudpickle >=1.3.0 + - fsspec >=0.6.0 + - cytoolz >=0.8.2 + - scikit-learn >=0.22 + - pyyaml >=5.3.1 + - tqdm + - umap-learn + - numexpr + - distributed + - dask[complete] + - attrs + - boltons + - requests + - pip: + - arboreto==0.1.6 + - interlap==0.2.7 + - multiprocessing_on_dill==3.5.0a4 + - ctxcore==0.2.0 + +test: + imports: + - pyscenic + +about: + home: https://github.com/aertslab/pySCENIC + summary: 'pySCENIC is a python implementation of the SCENIC pipeline' + license: MIT + license_family: MIT + +extra: + recipe-maintainers: + - pcm32 \ No newline at end of file From fb12e0db44f9702de7df6d34479ad032d27852bd Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 11:51:24 +0200 Subject: [PATCH 02/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 20 +++++++++----------- 1 file changed, 9 insertions(+), 11 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 7a25e71929684..923ab40690d85 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -7,15 +7,13 @@ package: version: {{ version }} source: - - url: https://pypi.io/packages/source/p/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: {{ sha256 }} - folder: pyscenic-0.12.1 + url: https://pypi.io/packages/source/p/{{ name }}/{{ name }}-{{ version }}.tar.gz + sha256: {{ sha256 }} build: number: 0 noarch: python - run_exports: - - {{ pin_subpackage(name, max_pin='x') }} + script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" requirements: host: @@ -52,11 +50,11 @@ requirements: - attrs - boltons - requests - - pip: - - arboreto==0.1.6 - - interlap==0.2.7 - - multiprocessing_on_dill==3.5.0a4 - - ctxcore==0.2.0 + pip: + - arboreto==0.1.6 + - interlap==0.2.7 + - multiprocessing_on_dill==3.5.0a4 + - ctxcore==0.2.0 test: imports: @@ -70,4 +68,4 @@ about: extra: recipe-maintainers: - - pcm32 \ No newline at end of file + - pcm32 From d77b6a1975375ffe326d7d60581f2ed5b6be371b Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 12:05:31 +0200 Subject: [PATCH 03/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 923ab40690d85..5ebb3b141c602 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -13,11 +13,12 @@ source: build: number: 0 noarch: python - script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv" + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} requirements: host: - - python=3.10 + - python >=3.10 - pip - setuptools_scm - dask[complete] @@ -28,7 +29,7 @@ requirements: - scipy - {{ compiler('c') }} run: - - python=3.10 + - python >=3.10 - aiohttp - frozendict - numpy >=1.19 @@ -51,10 +52,10 @@ requirements: - boltons - requests pip: - - arboreto==0.1.6 - - interlap==0.2.7 - - multiprocessing_on_dill==3.5.0a4 - - ctxcore==0.2.0 + - arboreto ==0.1.6 + - interlap ==0.2.7 + - multiprocessing_on_dill ==3.5.0a4 + - ctxcore ==0.2.0 test: imports: From a7919aa68daf842d14b429faa32bff1bfc782440 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 12:11:38 +0200 Subject: [PATCH 04/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 5ebb3b141c602..740c6ded3b24e 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -12,12 +12,12 @@ source: build: number: 0 - noarch: python run_exports: - {{ pin_subpackage(name, max_pin='x') }} requirements: - host: + build: + - {{ compiler('c') }} - python >=3.10 - pip - setuptools_scm @@ -27,7 +27,6 @@ requirements: - pandas - scikit-learn - scipy - - {{ compiler('c') }} run: - python >=3.10 - aiohttp From c96f7c394749935f1c4745478d2d177d34745730 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 16:39:23 +0200 Subject: [PATCH 05/69] Delete recipes/pyscenic/build.sh --- recipes/pyscenic/build.sh | 31 ------------------------------- 1 file changed, 31 deletions(-) delete mode 100644 recipes/pyscenic/build.sh diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh deleted file mode 100644 index ff07df22a6eea..0000000000000 --- a/recipes/pyscenic/build.sh +++ /dev/null @@ -1,31 +0,0 @@ -#!/bin/bash -set -ex - -if [ -z "${PYTHON}" ]; then - PYTHON=$(which python) -fi - - -pushd ${SRC_DIR}/pyscenic-0.12.1 -${PYTHON} -m pip install . --no-deps --ignore-installed -vv -popd - -for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0 -do - pushd ${SRC_DIR}/${package} - - if [ "$package" == "arboreto-0.1.6" ]; then - if [ ! -f requirements.txt ]; then - echo "Creating requirements.txt for arboreto" - echo "dask[complete]" > requirements.txt - echo "distributed" >> requirements.txt - echo "numpy>=1.16.5" >> requirements.txt - echo "pandas" >> requirements.txt - echo "scikit-learn" >> requirements.txt - echo "scipy" >> requirements.txt - fi - fi - - ${PYTHON} -m pip install --use-pep517 -vv --no-deps . - popd -done From bda27f2dc2041e5c542370438b65c2e590f5a929 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 16:40:49 +0200 Subject: [PATCH 06/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 145 ++++++++++++++++++++++--------------- 1 file changed, 88 insertions(+), 57 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 740c6ded3b24e..4c61fa1c39b13 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -1,71 +1,102 @@ {% set name = "pyscenic" %} {% set version = "0.12.1" %} -{% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} package: - name: {{ name }} - version: {{ version }} +name: "{{ name|lower }}" +version: "{{ version }}" source: - url: https://pypi.io/packages/source/p/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: {{ sha256 }} +url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" +sha256: ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2 build: - number: 0 - run_exports: - - {{ pin_subpackage(name, max_pin='x') }} +number: 0 +entry_points: + - pyscenic = pyscenic.cli.pyscenic:main + - db2feather = pyscenic.cli.db2feather:main + - csv2loom = pyscenic.cli.csv2loom:main + - invertdb = pyscenic.cli.invertdb:main + - gmt2regions = pyscenic.cli.gmt2regions:main +script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" requirements: - build: - - {{ compiler('c') }} - - python >=3.10 - - pip - - setuptools_scm - - dask[complete] - - distributed - - numpy >=1.16.5 - - pandas - - scikit-learn - - scipy - run: - - python >=3.10 - - aiohttp - - frozendict - - numpy >=1.19 - - pandas >=1.3 - - scipy >=1.6 - - llvmlite >=0.34 - - numba >=0.51.2 - - click >=7.0 - - cloudpickle >=1.3.0 - - fsspec >=0.6.0 - - cytoolz >=0.8.2 - - scikit-learn >=0.22 - - pyyaml >=5.3.1 - - tqdm - - umap-learn - - numexpr - - distributed - - dask[complete] - - attrs - - boltons - - requests - pip: - - arboreto ==0.1.6 - - interlap ==0.2.7 - - multiprocessing_on_dill ==3.5.0a4 - - ctxcore ==0.2.0 +host: + - aiohttp + - arboreto >=0.1.6 + - attrs + - boltons + - cloudpickle + - ctxcore >=0.2.0 + - cytoolz + - dask + - distributed + - frozendict + - fsspec + - interlap + - llvmlite + - loompy + - multiprocessing_on_dill + - networkx + - numba >=0.51.2 + - numexpr + - numpy + - pandas >=1.3.5 + - pip + - python + - pyyaml + - requests + - scikit-learn >=0.22.2 + - scipy + - setuptools + - tqdm + - umap-learn +run: + - aiohttp + - arboreto >=0.1.6 + - attrs + - boltons + - cloudpickle + - ctxcore >=0.2.0 + - cytoolz + - dask + - distributed + - frozendict + - fsspec + - interlap + - llvmlite + - loompy + - multiprocessing_on_dill + - networkx + - numba >=0.51.2 + - numexpr + - numpy + - pandas >=1.3.5 + - python + - pyyaml + - requests + - scikit-learn >=0.22.2 + - scipy + - setuptools + - tqdm + - umap-learn test: - imports: - - pyscenic +imports: + - pyscenic + - pyscenic.cli + - resources + - resources.delineations + - resources.tests +commands: + - pyscenic --help + - db2feather --help + - csv2loom --help + - invertdb --help + - gmt2regions --help about: - home: https://github.com/aertslab/pySCENIC - summary: 'pySCENIC is a python implementation of the SCENIC pipeline' - license: MIT - license_family: MIT - -extra: - recipe-maintainers: - - pcm32 +home: "https://github.com/aertslab/pySCENIC" +license: "GNU General Public v3 or later (GPLv3+)" +license_family: GPL3 +license_file: +summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." From 40cafecc39d128063b8b769d6483eceb6ca1e297 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 16:50:54 +0200 Subject: [PATCH 07/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 171 ++++++++++++++++++------------------- 1 file changed, 83 insertions(+), 88 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 4c61fa1c39b13..72ba02e37c33e 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -2,101 +2,96 @@ {% set version = "0.12.1" %} package: -name: "{{ name|lower }}" -version: "{{ version }}" + name: "{{ name|lower }}" + version: "{{ version }}" source: -url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" -sha256: ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2 + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2 build: -number: 0 -entry_points: - - pyscenic = pyscenic.cli.pyscenic:main - - db2feather = pyscenic.cli.db2feather:main - - csv2loom = pyscenic.cli.csv2loom:main - - invertdb = pyscenic.cli.invertdb:main - - gmt2regions = pyscenic.cli.gmt2regions:main -script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + number: 0 + entry_points: + - pyscenic = pyscenic.cli.pyscenic:main + - db2feather = pyscenic.cli.db2feather:main + - csv2loom = pyscenic.cli.csv2loom:main + - invertdb = pyscenic.cli.invertdb:main + - gmt2regions = pyscenic.cli.gmt2regions:main + script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" requirements: -host: - - aiohttp - - arboreto >=0.1.6 - - attrs - - boltons - - cloudpickle - - ctxcore >=0.2.0 - - cytoolz - - dask - - distributed - - frozendict - - fsspec - - interlap - - llvmlite - - loompy - - multiprocessing_on_dill - - networkx - - numba >=0.51.2 - - numexpr - - numpy - - pandas >=1.3.5 - - pip - - python - - pyyaml - - requests - - scikit-learn >=0.22.2 - - scipy - - setuptools - - tqdm - - umap-learn -run: - - aiohttp - - arboreto >=0.1.6 - - attrs - - boltons - - cloudpickle - - ctxcore >=0.2.0 - - cytoolz - - dask - - distributed - - frozendict - - fsspec - - interlap - - llvmlite - - loompy - - multiprocessing_on_dill - - networkx - - numba >=0.51.2 - - numexpr - - numpy - - pandas >=1.3.5 - - python - - pyyaml - - requests - - scikit-learn >=0.22.2 - - scipy - - setuptools - - tqdm - - umap-learn + host: + - python + - pip + - setuptools + - numpy + - pandas >=1.3.5 + - scikit-learn >=0.22.2 + - scipy + - llvmlite + - numba >=0.51.2 + - numexpr + - cloudpickle + - fsspec + - cytoolz + - dask + - distributed + - attrs + - boltons + - tqdm + - umap-learn + - aiohttp + - arboreto >=0.1.6 + - ctxcore >=0.2.0 + - frozendict + - interlap + - loompy + - multiprocessing_on_dill + - networkx + - pyyaml + - requests + run: + - python + - numpy + - pandas >=1.3.5 + - scikit-learn >=0.22.2 + - scipy + - llvmlite + - numba >=0.51.2 + - numexpr + - cloudpickle + - fsspec + - cytoolz + - dask + - distributed + - attrs + - boltons + - tqdm + - umap-learn + - aiohttp + - arboreto >=0.1.6 + - ctxcore >=0.2.0 + - frozendict + - interlap + - loompy + - multiprocessing_on_dill + - networkx + - pyyaml + - requests test: -imports: - - pyscenic - - pyscenic.cli - - resources - - resources.delineations - - resources.tests -commands: - - pyscenic --help - - db2feather --help - - csv2loom --help - - invertdb --help - - gmt2regions --help + imports: + - pyscenic + - pyscenic.cli + commands: + - pyscenic --help + - db2feather --help + - csv2loom --help + - invertdb --help + - gmt2regions --help about: -home: "https://github.com/aertslab/pySCENIC" -license: "GNU General Public v3 or later (GPLv3+)" -license_family: GPL3 -license_file: -summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." + home: "https://github.com/aertslab/pySCENIC" + license: "GNU General Public v3 or later (GPLv3+)" + license_family: GPL3 + summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." From 7e781bebdd5db7e2658fa245a1c04e3eb2d07b0f Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 16:57:10 +0200 Subject: [PATCH 08/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 72ba02e37c33e..ea4f745fba42c 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -11,6 +11,7 @@ source: build: number: 0 + noarch: python entry_points: - pyscenic = pyscenic.cli.pyscenic:main - db2feather = pyscenic.cli.db2feather:main @@ -18,6 +19,8 @@ build: - invertdb = pyscenic.cli.invertdb:main - gmt2regions = pyscenic.cli.gmt2regions:main script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + run_exports: + - {{ pin_subpackage(name, max_pin='x') }} requirements: host: @@ -94,4 +97,10 @@ about: home: "https://github.com/aertslab/pySCENIC" license: "GNU General Public v3 or later (GPLv3+)" license_family: GPL3 - summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." + license_file: LICENSE # Add the actual license file here if it's included in the source + summary: "Python implementation of the SCENIC pipeline." + description: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." + +extra: + recipe-maintainers: + - pcm32 From 91f1071cbcff3e4e50090260a5d7fb440bdf4c67 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 19:20:50 +0200 Subject: [PATCH 09/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 75 ++++++++------------------------------ 1 file changed, 15 insertions(+), 60 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index ea4f745fba42c..9e265c53091c6 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -1,17 +1,13 @@ {% set name = "pyscenic" %} {% set version = "0.12.1" %} - package: name: "{{ name|lower }}" version: "{{ version }}" - source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2 - build: number: 0 - noarch: python entry_points: - pyscenic = pyscenic.cli.pyscenic:main - db2feather = pyscenic.cli.db2feather:main @@ -19,88 +15,47 @@ build: - invertdb = pyscenic.cli.invertdb:main - gmt2regions = pyscenic.cli.gmt2regions:main script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" - run_exports: - - {{ pin_subpackage(name, max_pin='x') }} - requirements: host: - python - pip - setuptools - - numpy - - pandas >=1.3.5 - - scikit-learn >=0.22.2 - - scipy - - llvmlite - - numba >=0.51.2 - - numexpr + - wheel + run: + - aiohttp + - arboreto >=0.1.6 + - attrs + - boltons - cloudpickle - - fsspec + - ctxcore >=0.2.0 - cytoolz - dask - distributed - - attrs - - boltons - - tqdm - - umap-learn - - aiohttp - - arboreto >=0.1.6 - - ctxcore >=0.2.0 - frozendict + - fsspec - interlap + - llvmlite - loompy - multiprocessing_on_dill - networkx - - pyyaml - - requests - run: - - python + - numba >=0.51.2 + - numexpr - numpy - pandas >=1.3.5 + - python + - pyyaml + - requests - scikit-learn >=0.22.2 - scipy - - llvmlite - - numba >=0.51.2 - - numexpr - - cloudpickle - - fsspec - - cytoolz - - dask - - distributed - - attrs - - boltons - tqdm - umap-learn - - aiohttp - - arboreto >=0.1.6 - - ctxcore >=0.2.0 - - frozendict - - interlap - - loompy - - multiprocessing_on_dill - - networkx - - pyyaml - - requests - test: imports: - pyscenic - pyscenic.cli commands: - pyscenic --help - - db2feather --help - - csv2loom --help - - invertdb --help - - gmt2regions --help - about: home: "https://github.com/aertslab/pySCENIC" license: "GNU General Public v3 or later (GPLv3+)" - license_family: GPL3 - license_file: LICENSE # Add the actual license file here if it's included in the source - summary: "Python implementation of the SCENIC pipeline." - description: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." - -extra: - recipe-maintainers: - - pcm32 + summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." From ba4e0793a95f633068cce797d67de64dc3e35429 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 2 Sep 2024 19:35:10 +0200 Subject: [PATCH 10/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 9e265c53091c6..c6f26619ade3f 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -8,6 +8,9 @@ source: sha256: ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2 build: number: 0 + noarch: generic + run_exports: + - {{ pin_subpackage(name, max_pin="x.x") }} entry_points: - pyscenic = pyscenic.cli.pyscenic:main - db2feather = pyscenic.cli.db2feather:main @@ -58,4 +61,11 @@ test: about: home: "https://github.com/aertslab/pySCENIC" license: "GNU General Public v3 or later (GPLv3+)" - summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." + license_family: GPL3 + license_file: "LICENSE" + summary: "Python implementation of the SCENIC pipeline." + description: | + pySCENIC is a Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments. +extra: + recipe-maintainers: + - 179018299 From 27d5c50590a7c6640e19ac88d11c7d6023b92cd1 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 3 Sep 2024 15:49:06 +0200 Subject: [PATCH 11/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index c6f26619ade3f..76a29499c718f 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -17,7 +17,9 @@ build: - csv2loom = pyscenic.cli.csv2loom:main - invertdb = pyscenic.cli.invertdb:main - gmt2regions = pyscenic.cli.gmt2regions:main - script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + script: + - "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + - "{{ PYTHON }} -m pip install arboreto interlap multiprocessing_on_dill ctxcore -vv" requirements: host: - python @@ -26,20 +28,16 @@ requirements: - wheel run: - aiohttp - - arboreto >=0.1.6 - attrs - boltons - cloudpickle - - ctxcore >=0.2.0 - cytoolz - dask - distributed - frozendict - fsspec - - interlap - llvmlite - loompy - - multiprocessing_on_dill - networkx - numba >=0.51.2 - numexpr @@ -66,6 +64,3 @@ about: summary: "Python implementation of the SCENIC pipeline." description: | pySCENIC is a Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments. -extra: - recipe-maintainers: - - 179018299 From 630446eadd995eefa3ec92bd7b912b85a347e039 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 3 Sep 2024 17:21:23 +0200 Subject: [PATCH 12/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 76a29499c718f..3f5c19c399f3f 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -18,9 +18,13 @@ build: - invertdb = pyscenic.cli.invertdb:main - gmt2regions = pyscenic.cli.gmt2regions:main script: - - "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" - "{{ PYTHON }} -m pip install arboreto interlap multiprocessing_on_dill ctxcore -vv" + - "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" requirements: + build: + - make + - {{ compiler('c') }} + - {{ compiler('cxx') }} host: - python - pip From e64ed57d1a5c9a43e9d376106665e2922ccc0840 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 3 Sep 2024 17:30:06 +0200 Subject: [PATCH 13/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 33 ++++++++++++++++++++------------- 1 file changed, 20 insertions(+), 13 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 3f5c19c399f3f..da3e2ac4b7ab6 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -1,65 +1,72 @@ {% set name = "pyscenic" %} {% set version = "0.12.1" %} +{% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} + package: name: "{{ name|lower }}" version: "{{ version }}" + source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2 + sha256: {{ sha256 }} + build: number: 0 - noarch: generic run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - entry_points: - - pyscenic = pyscenic.cli.pyscenic:main - - db2feather = pyscenic.cli.db2feather:main - - csv2loom = pyscenic.cli.csv2loom:main - - invertdb = pyscenic.cli.invertdb:main - - gmt2regions = pyscenic.cli.gmt2regions:main - script: - - "{{ PYTHON }} -m pip install arboreto interlap multiprocessing_on_dill ctxcore -vv" - - "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + requirements: build: - - make - {{ compiler('c') }} - {{ compiler('cxx') }} + - make + - python + - pip + - setuptools + - wheel + host: - python - pip - setuptools - wheel + run: + - python - aiohttp + - arboreto >=0.1.6 - attrs - boltons - cloudpickle + - ctxcore >=0.2.0 - cytoolz - dask - distributed - frozendict - fsspec + - interlap - llvmlite - loompy + - multiprocessing_on_dill - networkx - numba >=0.51.2 - numexpr - numpy - pandas >=1.3.5 - - python - pyyaml - requests - scikit-learn >=0.22.2 - scipy - tqdm - umap-learn + test: imports: - pyscenic - pyscenic.cli commands: - pyscenic --help + about: home: "https://github.com/aertslab/pySCENIC" license: "GNU General Public v3 or later (GPLv3+)" From 01766c359b315444fb911d9e6eb70523696b7857 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 4 Sep 2024 16:10:33 +0200 Subject: [PATCH 14/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index da3e2ac4b7ab6..8915f75781fd0 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -7,8 +7,21 @@ package: version: "{{ version }}" source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: {{ sha256 }} + - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: {{ sha256 }} + folder: pyscenic-0.12.1 + - url: "https://files.pythonhosted.org/packages/source/a/arboreto/arboreto-0.1.6.tar.gz" + sha256: 32fdac5e8a3e0ef2e196b5827f067d815ac4e689d2fca0dc437f42abdeeb89ab + folder: arboreto-0.1.6 + - url: "https://files.pythonhosted.org/packages/source/i/interlap/interlap-0.2.7.tar.gz" + sha256: 31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9 + folder: interlap-0.2.7 + - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" + sha256: d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7 + folder: multiprocessing_on_dill-3.5.0a4 + - url: "https://github.com/aertslab/ctxcore/archive/refs/tags/0.2.0.tar.gz" + sha256: a7ebf0f2625641b76a390993e12042e92fff7d0ac242c7fad5e3bff3ff3cd67a + folder: ctxcore-0.2.0 build: number: 0 From 7e4b20ab7eb044e3e2cf77cd280ce1a0a6ce31b1 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 4 Sep 2024 16:35:57 +0200 Subject: [PATCH 15/69] Add files via upload --- recipes/pyscenic/build.sh | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 recipes/pyscenic/build.sh diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh new file mode 100644 index 0000000000000..c8b5c2cb5b957 --- /dev/null +++ b/recipes/pyscenic/build.sh @@ -0,0 +1,14 @@ +#!/bin/bash +set -ex + +# Compile and install the sources in the order required +for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do + pushd ${SRC_DIR}/${package} + ${PYTHON} -m pip install . --no-deps --ignore-installed -vv + popd +done + +# Finally, install the main package +pushd ${SRC_DIR}/pyscenic-0.12.1 +${PYTHON} -m pip install . --no-deps --ignore-installed -vv +popd From 61e9c0c62de6610e8f23fb1fbac4dbc81cbdaf75 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 4 Sep 2024 17:14:36 +0200 Subject: [PATCH 16/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 8915f75781fd0..f8b7e37fff158 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -27,6 +27,7 @@ build: number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} + script: bash ./build.sh requirements: build: @@ -47,20 +48,16 @@ requirements: run: - python - aiohttp - - arboreto >=0.1.6 - attrs - boltons - cloudpickle - - ctxcore >=0.2.0 - cytoolz - dask - distributed - frozendict - fsspec - - interlap - llvmlite - loompy - - multiprocessing_on_dill - networkx - numba >=0.51.2 - numexpr @@ -88,3 +85,7 @@ about: summary: "Python implementation of the SCENIC pipeline." description: | pySCENIC is a Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments. + +extra: + recipe-maintainers: + - 179018299 From cbb55429e73aa973cd1790365d451bbf0c3674c2 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 4 Sep 2024 17:15:00 +0200 Subject: [PATCH 17/69] Update build.sh --- recipes/pyscenic/build.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index c8b5c2cb5b957..a75b7bc422289 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -1,14 +1,12 @@ #!/bin/bash set -ex -# Compile and install the sources in the order required for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do pushd ${SRC_DIR}/${package} ${PYTHON} -m pip install . --no-deps --ignore-installed -vv popd done -# Finally, install the main package pushd ${SRC_DIR}/pyscenic-0.12.1 ${PYTHON} -m pip install . --no-deps --ignore-installed -vv popd From c1b09019767e6aa69cdf8a5aad78d994076ff248 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 4 Sep 2024 17:39:03 +0200 Subject: [PATCH 18/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index f8b7e37fff158..10ee133157620 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -27,7 +27,6 @@ build: number: 0 run_exports: - {{ pin_subpackage(name, max_pin="x.x") }} - script: bash ./build.sh requirements: build: From 20738d252114e2a5ed6230cd696772d922ed0560 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 4 Sep 2024 21:43:45 +0200 Subject: [PATCH 19/69] Update build.sh --- recipes/pyscenic/build.sh | 30 ++++++++++++++++++++++++------ 1 file changed, 24 insertions(+), 6 deletions(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index a75b7bc422289..f558d53515f7b 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -1,11 +1,29 @@ #!/bin/bash -set -ex +set -e -for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do - pushd ${SRC_DIR}/${package} - ${PYTHON} -m pip install . --no-deps --ignore-installed -vv - popd -done +pushd ${SRC_DIR}/arboreto-0.1.6 +if [ ! -f requirements.txt ]; then + echo "dask[complete]" > requirements.txt + echo "distributed" >> requirements.txt + echo "numpy>=1.16.5" >> requirements.txt + echo "pandas" >> requirements.txt + echo "scikit-learn" >> requirements.txt + echo "scipy" >> requirements.txt +fi +${PYTHON} -m pip install . --no-deps --ignore-installed -vv +popd + +pushd ${SRC_DIR}/interlap-0.2.7 +${PYTHON} -m pip install . --no-deps --ignore-installed -vv +popd + +pushd ${SRC_DIR}/multiprocessing_on_dill-3.5.0a4 +${PYTHON} -m pip install . --no-deps --ignore-installed -vv +popd + +pushd ${SRC_DIR}/ctxcore-0.2.0 +${PYTHON} -m pip install . --no-deps --ignore-installed -vv +popd pushd ${SRC_DIR}/pyscenic-0.12.1 ${PYTHON} -m pip install . --no-deps --ignore-installed -vv From 5af301eb6938a5421bd0b45a217853c0f84fd16f Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 09:52:40 +0200 Subject: [PATCH 20/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 10ee133157620..44a52e2a1ce6d 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -37,12 +37,14 @@ requirements: - pip - setuptools - wheel + - setuptools_scm host: - python - pip - setuptools - wheel + - setuptools_scm run: - python @@ -68,6 +70,11 @@ requirements: - scipy - tqdm - umap-learn + - pip: + - arboreto + - interlap + - multiprocessing_on_dill + - ctxcore test: imports: @@ -84,7 +91,6 @@ about: summary: "Python implementation of the SCENIC pipeline." description: | pySCENIC is a Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments. - extra: recipe-maintainers: - 179018299 From e38ae0fc38bacba70b09e139c1ec40165e62b0a5 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 09:59:46 +0200 Subject: [PATCH 21/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 44a52e2a1ce6d..bba978d69a6f1 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -8,43 +8,42 @@ package: source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: {{ sha256 }} + sha256: "{{ sha256 }}" folder: pyscenic-0.12.1 - url: "https://files.pythonhosted.org/packages/source/a/arboreto/arboreto-0.1.6.tar.gz" - sha256: 32fdac5e8a3e0ef2e196b5827f067d815ac4e689d2fca0dc437f42abdeeb89ab + sha256: "32fdac5e8a3e0ef2e196b5827f067d815ac4e689d2fca0dc437f42abdeeb89ab" folder: arboreto-0.1.6 - url: "https://files.pythonhosted.org/packages/source/i/interlap/interlap-0.2.7.tar.gz" - sha256: 31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9 + sha256: "31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9" folder: interlap-0.2.7 - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" - sha256: d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7 + sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7" folder: multiprocessing_on_dill-3.5.0a4 - url: "https://github.com/aertslab/ctxcore/archive/refs/tags/0.2.0.tar.gz" - sha256: a7ebf0f2625641b76a390993e12042e92fff7d0ac242c7fad5e3bff3ff3cd67a + sha256: "a7ebf0f2625641b76a390993e12042e92fff7d0ac242c7fad5e3bff3ff3cd67a" folder: ctxcore-0.2.0 build: number: 0 run_exports: - - {{ pin_subpackage(name, max_pin="x.x") }} + - "{{ pin_subpackage(name, max_pin='x.x') }}" requirements: build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} + - "{{ compiler('c') }}" + - "{{ compiler('cxx') }}" - make - python - pip - setuptools - wheel - - setuptools_scm + - setuptools_scm host: - python - pip - setuptools - wheel - - setuptools_scm run: - python @@ -70,11 +69,6 @@ requirements: - scipy - tqdm - umap-learn - - pip: - - arboreto - - interlap - - multiprocessing_on_dill - - ctxcore test: imports: From fa8c5119e4a18dc5652b421c954d615dc46b49e5 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 13:07:47 +0200 Subject: [PATCH 22/69] Update build.sh --- recipes/pyscenic/build.sh | 31 +++++++++---------------------- 1 file changed, 9 insertions(+), 22 deletions(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index f558d53515f7b..b57020c7b9f93 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -1,30 +1,17 @@ #!/bin/bash -set -e +set -ex -pushd ${SRC_DIR}/arboreto-0.1.6 -if [ ! -f requirements.txt ]; then - echo "dask[complete]" > requirements.txt - echo "distributed" >> requirements.txt - echo "numpy>=1.16.5" >> requirements.txt - echo "pandas" >> requirements.txt - echo "scikit-learn" >> requirements.txt - echo "scipy" >> requirements.txt +if [ -z "${PYTHON}" ]; then + PYTHON=$(which python) fi -${PYTHON} -m pip install . --no-deps --ignore-installed -vv -popd -pushd ${SRC_DIR}/interlap-0.2.7 -${PYTHON} -m pip install . --no-deps --ignore-installed -vv -popd +for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do + pushd ${SRC_DIR}/${package} + ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv + popd +done -pushd ${SRC_DIR}/multiprocessing_on_dill-3.5.0a4 -${PYTHON} -m pip install . --no-deps --ignore-installed -vv -popd - -pushd ${SRC_DIR}/ctxcore-0.2.0 -${PYTHON} -m pip install . --no-deps --ignore-installed -vv -popd pushd ${SRC_DIR}/pyscenic-0.12.1 -${PYTHON} -m pip install . --no-deps --ignore-installed -vv +${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd From 73f2370df310c4c27debcf3dfea9fe3da9a0268a Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 14:14:38 +0200 Subject: [PATCH 23/69] Update build.sh --- recipes/pyscenic/build.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index b57020c7b9f93..b2cabddad3191 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -7,11 +7,11 @@ fi for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do pushd ${SRC_DIR}/${package} - ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv + ${PYTHON} -m pip install . --no-deps --ignore-installed -vv popd done - pushd ${SRC_DIR}/pyscenic-0.12.1 -${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv +${PYTHON} -m pip install . --no-deps --ignore-installed -vv popd + From 41d453b70b2accf9f88df04c6a519375396c17de Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 15:09:27 +0200 Subject: [PATCH 24/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index bba978d69a6f1..0f9be9177b3cb 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -77,14 +77,6 @@ test: commands: - pyscenic --help -about: - home: "https://github.com/aertslab/pySCENIC" - license: "GNU General Public v3 or later (GPLv3+)" - license_family: GPL3 - license_file: "LICENSE" - summary: "Python implementation of the SCENIC pipeline." - description: | - pySCENIC is a Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments. extra: recipe-maintainers: - 179018299 From 688d373f7f7962e09501de4c529741539858165e Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 15:10:23 +0200 Subject: [PATCH 25/69] Update build.sh --- recipes/pyscenic/build.sh | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index b2cabddad3191..7fe8c4ebc75a3 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -7,11 +7,20 @@ fi for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do pushd ${SRC_DIR}/${package} - ${PYTHON} -m pip install . --no-deps --ignore-installed -vv + + if [ "$package" == "arboreto-0.1.6" ] && [ ! -f requirements.txt ]; then + echo "dask[complete]" > requirements.txt + echo "distributed" >> requirements.txt + echo "numpy>=1.16.5" >> requirements.txt + echo "pandas" >> requirements.txt + echo "scikit-learn" >> requirements.txt + echo "scipy" >> requirements.txt + fi + + ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd done pushd ${SRC_DIR}/pyscenic-0.12.1 -${PYTHON} -m pip install . --no-deps --ignore-installed -vv +${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd - From 33305a83e3debac975870b2c84512d054b40e703 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 15:29:48 +0200 Subject: [PATCH 26/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 0f9be9177b3cb..7b403344262fd 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -77,6 +77,11 @@ test: commands: - pyscenic --help +about: + home: https://github.com/aertslab/pySCENIC + summary: 'pySCENIC is a python implementation of the SCENIC pipeline' + license: MIT + license_family: MIT extra: recipe-maintainers: - 179018299 From a682b7420fa035520a1673c351155bed8230c3ad Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 15:50:30 +0200 Subject: [PATCH 27/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 7b403344262fd..2169117fa150d 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -53,6 +53,7 @@ requirements: - cloudpickle - cytoolz - dask + - dill - distributed - frozendict - fsspec From 4a6664af10111cb72316a241d53e4f9523e81aee Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 16:53:15 +0200 Subject: [PATCH 28/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 3 --- 1 file changed, 3 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 2169117fa150d..be60560bff616 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -74,9 +74,6 @@ requirements: test: imports: - pyscenic - - pyscenic.cli - commands: - - pyscenic --help about: home: https://github.com/aertslab/pySCENIC From fcf15bcd7c54f43cad62b6428dfc912d258eca34 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 20:42:33 +0200 Subject: [PATCH 29/69] Update meta.yaml From d65d7210163e8cdaaee4c68bf864ac2a38571838 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 5 Sep 2024 20:43:22 +0200 Subject: [PATCH 30/69] Update build.sh From cfe4b928adcc61c2384f85d0617dba5d5540bb93 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 11 Sep 2024 12:03:14 +0200 Subject: [PATCH 31/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index be60560bff616..17b0df3290bb6 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -33,27 +33,27 @@ requirements: - "{{ compiler('c') }}" - "{{ compiler('cxx') }}" - make - - python + - python >=3.10,<3.11 # Pinning Python version to 3.10 - pip - setuptools - wheel - setuptools_scm host: - - python + - python >=3.10,<3.11 # Pinning Python version to 3.10 - pip - setuptools - wheel run: - - python + - python >=3.10,<3.11 # Pinning Python version to 3.10 - aiohttp - attrs - boltons - cloudpickle - cytoolz - - dask - dill + - dask - distributed - frozendict - fsspec @@ -62,14 +62,15 @@ requirements: - networkx - numba >=0.51.2 - numexpr - - numpy - pandas >=1.3.5 - pyyaml - requests - - scikit-learn >=0.22.2 + - scikit-learn - scipy - tqdm - umap-learn + - numpy ==1.23.5 + - pyarrow test: imports: @@ -80,6 +81,7 @@ about: summary: 'pySCENIC is a python implementation of the SCENIC pipeline' license: MIT license_family: MIT + extra: recipe-maintainers: - 179018299 From 1af7f2d037ea86df0923bf92225919bc527b347b Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 11 Sep 2024 12:03:45 +0200 Subject: [PATCH 32/69] Update build.sh From e541c226258d8beb1a2e656cf78ccb1007d5aae4 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 12 Sep 2024 17:10:40 +0200 Subject: [PATCH 33/69] deleting packeges from conda --- recipes/pyscenic/build.sh | 12 ++---------- recipes/pyscenic/meta.yaml | 33 +++++++++++++++++---------------- 2 files changed, 19 insertions(+), 26 deletions(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index 7fe8c4ebc75a3..aaa8602a907b1 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -5,18 +5,9 @@ if [ -z "${PYTHON}" ]; then PYTHON=$(which python) fi -for package in arboreto-0.1.6 interlap-0.2.7 multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do +for package in multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do pushd ${SRC_DIR}/${package} - if [ "$package" == "arboreto-0.1.6" ] && [ ! -f requirements.txt ]; then - echo "dask[complete]" > requirements.txt - echo "distributed" >> requirements.txt - echo "numpy>=1.16.5" >> requirements.txt - echo "pandas" >> requirements.txt - echo "scikit-learn" >> requirements.txt - echo "scipy" >> requirements.txt - fi - ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd done @@ -24,3 +15,4 @@ done pushd ${SRC_DIR}/pyscenic-0.12.1 ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd + diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 17b0df3290bb6..49ab7c14d5266 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -10,51 +10,51 @@ source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: "{{ sha256 }}" folder: pyscenic-0.12.1 - - url: "https://files.pythonhosted.org/packages/source/a/arboreto/arboreto-0.1.6.tar.gz" - sha256: "32fdac5e8a3e0ef2e196b5827f067d815ac4e689d2fca0dc437f42abdeeb89ab" - folder: arboreto-0.1.6 - - url: "https://files.pythonhosted.org/packages/source/i/interlap/interlap-0.2.7.tar.gz" - sha256: "31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9" - folder: interlap-0.2.7 - - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" - sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7" - folder: multiprocessing_on_dill-3.5.0a4 + - url: "https://github.com/aertslab/ctxcore/archive/refs/tags/0.2.0.tar.gz" sha256: "a7ebf0f2625641b76a390993e12042e92fff7d0ac242c7fad5e3bff3ff3cd67a" folder: ctxcore-0.2.0 + - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" + sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7" + folder: multiprocessing_on_dill-3.5.0a4 build: number: 0 run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" + script_env: + - CONDA_BUILD_SYSROOT=/opt/conda/envs/sysroot + build_args: + - "-j2" requirements: build: - "{{ compiler('c') }}" - "{{ compiler('cxx') }}" - make - - python >=3.10,<3.11 # Pinning Python version to 3.10 + - python >=3.10,<3.11 - pip - setuptools - wheel - setuptools_scm host: - - python >=3.10,<3.11 # Pinning Python version to 3.10 + - python >=3.10,<3.11 - pip - setuptools - wheel run: - - python >=3.10,<3.11 # Pinning Python version to 3.10 + - python >=3.10,<3.11 - aiohttp + - arboreto - attrs - boltons - cloudpickle - cytoolz - dill - - dask - - distributed + - dask >=2023.4.1 + - distributed >=2023.4.1,<2023.5.0 - frozendict - fsspec - llvmlite @@ -70,8 +70,9 @@ requirements: - tqdm - umap-learn - numpy ==1.23.5 - - pyarrow - + - pyarrow + - interlap + - multiprocessing_on_dill test: imports: - pyscenic From 241cfea2e0ac46fd62a670b19c647aae44d97f9e Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 12 Sep 2024 17:11:56 +0200 Subject: [PATCH 34/69] error fix --- recipes/pyscenic/meta.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 49ab7c14d5266..2e7be97c7b9d9 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -72,7 +72,6 @@ requirements: - numpy ==1.23.5 - pyarrow - interlap - - multiprocessing_on_dill test: imports: - pyscenic From 621e4e219160d2ef4d2a3557a9a8027b2fbc6e2d Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 12 Sep 2024 23:47:47 +0200 Subject: [PATCH 35/69] Removed ctxcore and multiprocessing_on_dill from source --- recipes/pyscenic/meta.yaml | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 2e7be97c7b9d9..dd62c2f882268 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -11,21 +11,10 @@ source: sha256: "{{ sha256 }}" folder: pyscenic-0.12.1 - - url: "https://github.com/aertslab/ctxcore/archive/refs/tags/0.2.0.tar.gz" - sha256: "a7ebf0f2625641b76a390993e12042e92fff7d0ac242c7fad5e3bff3ff3cd67a" - folder: ctxcore-0.2.0 - - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" - sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7" - folder: multiprocessing_on_dill-3.5.0a4 - build: number: 0 run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" - script_env: - - CONDA_BUILD_SYSROOT=/opt/conda/envs/sysroot - build_args: - - "-j2" requirements: build: @@ -52,7 +41,7 @@ requirements: - boltons - cloudpickle - cytoolz - - dill + - dill - dask >=2023.4.1 - distributed >=2023.4.1,<2023.5.0 - frozendict @@ -72,6 +61,8 @@ requirements: - numpy ==1.23.5 - pyarrow - interlap + - ctxcore + test: imports: - pyscenic @@ -81,7 +72,3 @@ about: summary: 'pySCENIC is a python implementation of the SCENIC pipeline' license: MIT license_family: MIT - -extra: - recipe-maintainers: - - 179018299 From 222e3a5f8245b116db20fcd6a51caba7a607aa3a Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Fri, 13 Sep 2024 00:00:10 +0200 Subject: [PATCH 36/69] returned multiprocessing_on_dill --- recipes/pyscenic/build.sh | 9 +++------ recipes/pyscenic/meta.yaml | 4 ++++ 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index aaa8602a907b1..725efe4d7490d 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -5,12 +5,9 @@ if [ -z "${PYTHON}" ]; then PYTHON=$(which python) fi -for package in multiprocessing_on_dill-3.5.0a4 ctxcore-0.2.0; do - pushd ${SRC_DIR}/${package} - - ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv - popd -done +pushd ${SRC_DIR}/multiprocessing_on_dill-3.5.0a4 +${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv +popd pushd ${SRC_DIR}/pyscenic-0.12.1 ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index dd62c2f882268..10b6a023ce203 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -10,6 +10,10 @@ source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: "{{ sha256 }}" folder: pyscenic-0.12.1 + - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" + sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7" + folder: multiprocessing_on_dill-3.5.0a4 + build: number: 0 From 0d26c187da1ee54a63cb6b9d763aabbd9c33d1db Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Fri, 13 Sep 2024 00:07:54 +0200 Subject: [PATCH 37/69] fix an error --- recipes/pyscenic/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 10b6a023ce203..d13872f6c845c 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -10,7 +10,7 @@ source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: "{{ sha256 }}" folder: pyscenic-0.12.1 - - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" + - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7" folder: multiprocessing_on_dill-3.5.0a4 From 4efa1f2bf054cdc178ccf06572cfa855a6ec26cc Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Fri, 13 Sep 2024 00:27:15 +0200 Subject: [PATCH 38/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index d13872f6c845c..3c3b2b1677a94 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -19,6 +19,10 @@ build: number: 0 run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" + script_env: + - CONDA_BUILD_SYSROOT=/opt/conda/envs/sysroot + build_args: + - "-j2" requirements: build: From 42120e7d9508e76a176c809b7ec876f23cb3ef22 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 17 Sep 2024 15:05:11 +0200 Subject: [PATCH 39/69] test --- recipes/pyscenic/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 3c3b2b1677a94..87860064d36c3 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -70,6 +70,7 @@ requirements: - pyarrow - interlap - ctxcore + - multiprocessing_on_dill test: imports: From 9d0b5a2d1a6e9b56c67779d3712354915fa00d47 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 17 Sep 2024 15:21:55 +0200 Subject: [PATCH 40/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 87860064d36c3..d13872f6c845c 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -19,10 +19,6 @@ build: number: 0 run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" - script_env: - - CONDA_BUILD_SYSROOT=/opt/conda/envs/sysroot - build_args: - - "-j2" requirements: build: @@ -70,7 +66,6 @@ requirements: - pyarrow - interlap - ctxcore - - multiprocessing_on_dill test: imports: From 61f1c05ad580f0df6c6be546ffef20d25ac7f1d5 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 19 Sep 2024 15:21:44 +0200 Subject: [PATCH 41/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index d13872f6c845c..c04b496d7e397 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -10,15 +10,14 @@ source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: "{{ sha256 }}" folder: pyscenic-0.12.1 - - url: "https://files.pythonhosted.org/packages/source/m/multiprocessing_on_dill/multiprocessing_on_dill-3.5.0a4.tar.gz" - sha256: "d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7" - folder: multiprocessing_on_dill-3.5.0a4 - build: number: 0 run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" + script: | + patch -p1 < ${RECIPE_DIR}/my_patch.patch + python setup.py install requirements: build: From 2c107d05631ea7766e5a322f471cc3cdef58649c Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 19 Sep 2024 15:24:26 +0200 Subject: [PATCH 42/69] adding patch file --- recipes/pyscenic/dill_patch.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 recipes/pyscenic/dill_patch.patch diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch new file mode 100644 index 0000000000000..08a043dda42ef --- /dev/null +++ b/recipes/pyscenic/dill_patch.patch @@ -0,0 +1,12 @@ +diff --git a/src/pyscenic/prune.py b/src/pyscenic/prune.py +index abcdef1..1234567 100644 +--- a/src/pyscenic/prune.py ++++ b/src/pyscenic/prune.py +@@ -1,6 +1,6 @@ + +-from multiprocessing_on_dill.connection import Pipe +-from multiprocessing_on_dill.context import Process ++from multiprocessing.connection import Pipe ++from multiprocessing import Process + + From d8337b2a59d5b958596959ac62eec55156499d05 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 19 Sep 2024 15:25:10 +0200 Subject: [PATCH 43/69] error fix --- recipes/pyscenic/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index c04b496d7e397..d3ee945d05e32 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -16,7 +16,7 @@ build: run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" script: | - patch -p1 < ${RECIPE_DIR}/my_patch.patch + patch -p1 < ${RECIPE_DIR}/dill_patch.patch python setup.py install requirements: From a620bd03131ad2f8a0e84c96653bf9cff8b0725d Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 19 Sep 2024 15:25:29 +0200 Subject: [PATCH 44/69] Update build.sh --- recipes/pyscenic/build.sh | 3 --- 1 file changed, 3 deletions(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index 725efe4d7490d..66b6c235d876f 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -5,9 +5,6 @@ if [ -z "${PYTHON}" ]; then PYTHON=$(which python) fi -pushd ${SRC_DIR}/multiprocessing_on_dill-3.5.0a4 -${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv -popd pushd ${SRC_DIR}/pyscenic-0.12.1 ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv From 7a8e9bdfae0710636aa92b322a1b701d4ddfa03d Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 19 Sep 2024 15:40:08 +0200 Subject: [PATCH 45/69] fix patching --- recipes/pyscenic/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index d3ee945d05e32..9067bda6558ce 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -16,8 +16,8 @@ build: run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" script: | - patch -p1 < ${RECIPE_DIR}/dill_patch.patch - python setup.py install + patch -p1 < ${RECIPE_DIR}/dill_patch.patch + $PYTHON setup.py install --single-version-externally-managed --record=record.txt requirements: build: From 49f288d0bdfce22ea233d1c05a3de68d8b980e35 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Sun, 22 Sep 2024 23:34:53 +0200 Subject: [PATCH 46/69] change source file --- recipes/pyscenic/dill_patch.patch | 2 ++ recipes/pyscenic/meta.yaml | 7 +++++-- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch index 08a043dda42ef..e0f367bfd8c5f 100644 --- a/recipes/pyscenic/dill_patch.patch +++ b/recipes/pyscenic/dill_patch.patch @@ -10,3 +10,5 @@ index abcdef1..1234567 100644 +from multiprocessing import Process + + diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 9067bda6558ce..ddca5498c828f 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -11,14 +11,17 @@ source: sha256: "{{ sha256 }}" folder: pyscenic-0.12.1 + + build: number: 0 run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" script: | - patch -p1 < ${RECIPE_DIR}/dill_patch.patch - $PYTHON setup.py install --single-version-externally-managed --record=record.txt + patch -p1 < ${RECIPE_DIR}/dill_patch.patch + $PYTHON setup.py install --single-version-externally-managed --record=record.txt + requirements: build: - "{{ compiler('c') }}" From 70cae7a4be0aa24253a034c6c7771e507537bd0e Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Mon, 23 Sep 2024 00:08:04 +0200 Subject: [PATCH 47/69] Delete recipes/pyscenic/build.sh --- recipes/pyscenic/build.sh | 12 ------------ 1 file changed, 12 deletions(-) delete mode 100644 recipes/pyscenic/build.sh diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh deleted file mode 100644 index 66b6c235d876f..0000000000000 --- a/recipes/pyscenic/build.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/bin/bash -set -ex - -if [ -z "${PYTHON}" ]; then - PYTHON=$(which python) -fi - - -pushd ${SRC_DIR}/pyscenic-0.12.1 -${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv -popd - From e94e23d4df334ad2bbfb941cc9c1aabfcfac1678 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 13:35:26 +0200 Subject: [PATCH 48/69] deleted connection --- recipes/pyscenic/dill_patch.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch index e0f367bfd8c5f..dee94eb747f02 100644 --- a/recipes/pyscenic/dill_patch.patch +++ b/recipes/pyscenic/dill_patch.patch @@ -6,7 +6,7 @@ index abcdef1..1234567 100644 -from multiprocessing_on_dill.connection import Pipe -from multiprocessing_on_dill.context import Process -+from multiprocessing.connection import Pipe ++from multiprocessing import Pipe +from multiprocessing import Process From 1d420f62b8cb603f6f508181a9562bb86a252d42 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 15:50:00 +0200 Subject: [PATCH 49/69] change path --- recipes/pyscenic/meta.yaml | 25 +++++++++++-------------- 1 file changed, 11 insertions(+), 14 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index ddca5498c828f..adce2e3f2a46b 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -9,29 +9,26 @@ package: source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: "{{ sha256 }}" - folder: pyscenic-0.12.1 - - + folder: pyscenic-{{ version }} build: number: 0 run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" script: | - patch -p1 < ${RECIPE_DIR}/dill_patch.patch - $PYTHON setup.py install --single-version-externally-managed --record=record.txt - + pushd ${SRC_DIR}/pyscenic-{{ version }} + patch -p1 < ${RECIPE_DIR}/my_patch.patch + ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv + popd + + requirements: build: - - "{{ compiler('c') }}" - - "{{ compiler('cxx') }}" - - make - python >=3.10,<3.11 - pip - setuptools - wheel - - setuptools_scm host: - python >=3.10,<3.11 @@ -42,12 +39,12 @@ requirements: run: - python >=3.10,<3.11 - aiohttp - - arboreto + - arboreto - attrs - boltons - cloudpickle - cytoolz - - dill + - dill - dask >=2023.4.1 - distributed >=2023.4.1,<2023.5.0 - frozendict @@ -66,8 +63,8 @@ requirements: - umap-learn - numpy ==1.23.5 - pyarrow - - interlap - - ctxcore + - interlap + - ctxcore test: imports: From cceb9274fd6411148d4ec791b534404c8a9bd441 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 15:50:45 +0200 Subject: [PATCH 50/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index adce2e3f2a46b..8048b801ef645 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -17,7 +17,7 @@ build: - "{{ pin_subpackage(name, max_pin='x.x') }}" script: | pushd ${SRC_DIR}/pyscenic-{{ version }} - patch -p1 < ${RECIPE_DIR}/my_patch.patch + patch -p1 < ${RECIPE_DIR}/dill_patch.patch ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd From a7b15b10558ce8aa12c557aa6cb60a40cd68cbe9 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 15:51:20 +0200 Subject: [PATCH 51/69] Update dill_patch.patch --- recipes/pyscenic/dill_patch.patch | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch index dee94eb747f02..73b986bbb397e 100644 --- a/recipes/pyscenic/dill_patch.patch +++ b/recipes/pyscenic/dill_patch.patch @@ -1,14 +1,8 @@ -diff --git a/src/pyscenic/prune.py b/src/pyscenic/prune.py -index abcdef1..1234567 100644 ---- a/src/pyscenic/prune.py -+++ b/src/pyscenic/prune.py -@@ -1,6 +1,6 @@ - +--- src/pyscenic/prune.py 2023-09-26 10:00:00.000000000 +0000 ++++ src/pyscenic/prune.py 2023-09-26 10:05:00.000000000 +0000 +@@ -1,2 +1,2 @@ -from multiprocessing_on_dill.connection import Pipe -from multiprocessing_on_dill.context import Process +from multiprocessing import Pipe +from multiprocessing import Process - - - From 3078e4fd979f641ca7203f802dacaf430b0b3846 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 15:59:30 +0200 Subject: [PATCH 52/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 8048b801ef645..00c7d5ad07cd1 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -13,15 +13,14 @@ source: build: number: 0 + noarch: python run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" script: | - pushd ${SRC_DIR}/pyscenic-{{ version }} patch -p1 < ${RECIPE_DIR}/dill_patch.patch + pushd ${SRC_DIR}/pyscenic-{{ version }} ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd - - requirements: build: From b4d55d912aad4d35214915a9c2cde0fb7a28a0e3 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 16:34:22 +0200 Subject: [PATCH 53/69] Delete recipes/pyscenic/dill_patch.patch --- recipes/pyscenic/dill_patch.patch | 8 -------- 1 file changed, 8 deletions(-) delete mode 100644 recipes/pyscenic/dill_patch.patch diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch deleted file mode 100644 index 73b986bbb397e..0000000000000 --- a/recipes/pyscenic/dill_patch.patch +++ /dev/null @@ -1,8 +0,0 @@ ---- src/pyscenic/prune.py 2023-09-26 10:00:00.000000000 +0000 -+++ src/pyscenic/prune.py 2023-09-26 10:05:00.000000000 +0000 -@@ -1,2 +1,2 @@ --from multiprocessing_on_dill.connection import Pipe --from multiprocessing_on_dill.context import Process -+from multiprocessing import Pipe -+from multiprocessing import Process - From fd83fbc9f6391eeaa572a035f427c1e15b408c9c Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 16:34:44 +0200 Subject: [PATCH 54/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 00c7d5ad07cd1..e602d0b969619 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -14,11 +14,10 @@ source: build: number: 0 noarch: python - run_exports: - - "{{ pin_subpackage(name, max_pin='x.x') }}" script: | - patch -p1 < ${RECIPE_DIR}/dill_patch.patch pushd ${SRC_DIR}/pyscenic-{{ version }} + sed -i 's/from multiprocessing_on_dill.connection import Pipe/from multiprocessing import Pipe/' src/pyscenic/prune.py + sed -i 's/from multiprocessing_on_dill.context import Process/from multiprocessing import Process/' src/pyscenic/prune.py ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd From fe2166e93693099707eb5a39bb297e28af461ce5 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 16:48:16 +0200 Subject: [PATCH 55/69] fix asincio error --- recipes/pyscenic/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index e602d0b969619..8cf83c1610732 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -20,6 +20,8 @@ build: sed -i 's/from multiprocessing_on_dill.context import Process/from multiprocessing import Process/' src/pyscenic/prune.py ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv popd + run_exports: + - {{ pin_subpackage(name, max_pin='x.x') }} requirements: build: From ace7c9878ad8c63992d5b37cdb4ad0752d670c32 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 22:47:03 +0200 Subject: [PATCH 56/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 11 +++-------- 1 file changed, 3 insertions(+), 8 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 8cf83c1610732..dc40a58224b1d 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -9,19 +9,14 @@ package: source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: "{{ sha256 }}" - folder: pyscenic-{{ version }} + - path: dill_patch.patch build: number: 0 noarch: python - script: | - pushd ${SRC_DIR}/pyscenic-{{ version }} - sed -i 's/from multiprocessing_on_dill.connection import Pipe/from multiprocessing import Pipe/' src/pyscenic/prune.py - sed -i 's/from multiprocessing_on_dill.context import Process/from multiprocessing import Process/' src/pyscenic/prune.py - ${PYTHON} -m pip install . --use-pep517 --no-deps --ignore-installed -vv - popd run_exports: - - {{ pin_subpackage(name, max_pin='x.x') }} + - "{{ pin_subpackage(name, max_pin='x.x') }}" + script: "{{ PYTHON }} -m pip install . -vv" requirements: build: From f68caceb28883ec30f2e02a49e64589c046ed3a6 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 22:53:06 +0200 Subject: [PATCH 57/69] Add files via upload --- recipes/pyscenic/dill_patch.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 recipes/pyscenic/dill_patch.patch diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch new file mode 100644 index 0000000000000..08a043dda42ef --- /dev/null +++ b/recipes/pyscenic/dill_patch.patch @@ -0,0 +1,12 @@ +diff --git a/src/pyscenic/prune.py b/src/pyscenic/prune.py +index abcdef1..1234567 100644 +--- a/src/pyscenic/prune.py ++++ b/src/pyscenic/prune.py +@@ -1,6 +1,6 @@ + +-from multiprocessing_on_dill.connection import Pipe +-from multiprocessing_on_dill.context import Process ++from multiprocessing.connection import Pipe ++from multiprocessing import Process + + From addf65689f37eeadf7ce842cba722790fcb85a4e Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Thu, 26 Sep 2024 23:00:39 +0200 Subject: [PATCH 58/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index dc40a58224b1d..e9b022baa3a49 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -1,6 +1,7 @@ {% set name = "pyscenic" %} {% set version = "0.12.1" %} {% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} +{% set patch_sha256 = "9e31c0fa80bf94481856d6670ad503ae1f40e32a654d03ed0fc757fba1bfee15" %} package: name: "{{ name|lower }}" @@ -10,6 +11,7 @@ source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" sha256: "{{ sha256 }}" - path: dill_patch.patch + sha256: "{{ patch_sha256 }}" build: number: 0 From fab1f611e781d216fca66931b4b405f79bb2d8f5 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 1 Oct 2024 12:31:10 +0200 Subject: [PATCH 59/69] test patching with sh script --- recipes/pyscenic/build.sh | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 recipes/pyscenic/build.sh diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh new file mode 100644 index 0000000000000..e5ff0368aebc8 --- /dev/null +++ b/recipes/pyscenic/build.sh @@ -0,0 +1,5 @@ +#!/bin/bash +set -e +patch -p1 < ${RECIPE_DIR}/dill_patch.patch + +$PYTHON -m pip install . --no-deps --ignore-installed -vv From c3de49f82bace3ed134356f58b660c1fab14824e Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 1 Oct 2024 12:32:05 +0200 Subject: [PATCH 60/69] Update meta.yaml with patch in sh --- recipes/pyscenic/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index e9b022baa3a49..e1f2e591e39e8 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -18,7 +18,7 @@ build: noarch: python run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" - script: "{{ PYTHON }} -m pip install . -vv" + script: bash ${RECIPE_DIR}/build.sh requirements: build: From 37f36eee0d799e1cf5e7db1d457dea7084b17b73 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 1 Oct 2024 13:06:53 +0200 Subject: [PATCH 61/69] Update build.sh --- recipes/pyscenic/build.sh | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh index e5ff0368aebc8..86fc6a3f49f84 100644 --- a/recipes/pyscenic/build.sh +++ b/recipes/pyscenic/build.sh @@ -1,5 +1,11 @@ #!/bin/bash -set -e +set -e +echo "Current working directory: $(pwd)" +echo "Listing files in working directory:" +ls -l +echo "Applying patch..." patch -p1 < ${RECIPE_DIR}/dill_patch.patch +echo "Patch applied, listing files:" +ls -l $PYTHON -m pip install . --no-deps --ignore-installed -vv From 129ffad67dc93e1e6c2c4830677811f71f752f20 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 1 Oct 2024 13:07:16 +0200 Subject: [PATCH 62/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index e1f2e591e39e8..30ac550dcf670 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -13,12 +13,6 @@ source: - path: dill_patch.patch sha256: "{{ patch_sha256 }}" -build: - number: 0 - noarch: python - run_exports: - - "{{ pin_subpackage(name, max_pin='x.x') }}" - script: bash ${RECIPE_DIR}/build.sh requirements: build: From 3798d9aa5e136a396d6d0da7d3c38f511b45e74f Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 1 Oct 2024 13:19:47 +0200 Subject: [PATCH 63/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 30ac550dcf670..249c815818492 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -13,6 +13,12 @@ source: - path: dill_patch.patch sha256: "{{ patch_sha256 }}" +build: + number: 0 + noarch: python + run_exports: + - "{{ pin_subpackage(name, max_pin='x.x') }}" + requirements: build: From 279610bce55c3be2110c19ca8f76621754793beb Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 1 Oct 2024 14:49:03 +0200 Subject: [PATCH 64/69] Delete recipes/pyscenic/build.sh --- recipes/pyscenic/build.sh | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 recipes/pyscenic/build.sh diff --git a/recipes/pyscenic/build.sh b/recipes/pyscenic/build.sh deleted file mode 100644 index 86fc6a3f49f84..0000000000000 --- a/recipes/pyscenic/build.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash -set -e -echo "Current working directory: $(pwd)" -echo "Listing files in working directory:" -ls -l -echo "Applying patch..." -patch -p1 < ${RECIPE_DIR}/dill_patch.patch - -echo "Patch applied, listing files:" -ls -l -$PYTHON -m pip install . --no-deps --ignore-installed -vv From b203376ad37e798329776200cb0f1cc68cfbc2e0 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Tue, 1 Oct 2024 14:49:27 +0200 Subject: [PATCH 65/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 249c815818492..911e84232d8a5 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -1,24 +1,23 @@ {% set name = "pyscenic" %} {% set version = "0.12.1" %} {% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} -{% set patch_sha256 = "9e31c0fa80bf94481856d6670ad503ae1f40e32a654d03ed0fc757fba1bfee15" %} package: name: "{{ name|lower }}" version: "{{ version }}" source: - - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "{{ sha256 }}" - - path: dill_patch.patch - sha256: "{{ patch_sha256 }}" + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: "{{ sha256 }}" + patches: + - dill_patch.patch build: - number: 0 + number: 0 noarch: python run_exports: - "{{ pin_subpackage(name, max_pin='x.x') }}" - + script: "{{ PYTHON }} -m pip install . -vv" requirements: build: From 1aa4448e9760900359786162440e07cb2f913b26 Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 2 Oct 2024 12:27:29 +0200 Subject: [PATCH 66/69] Update dill_patch.patch --- recipes/pyscenic/dill_patch.patch | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch index 08a043dda42ef..d94a8d43e4191 100644 --- a/recipes/pyscenic/dill_patch.patch +++ b/recipes/pyscenic/dill_patch.patch @@ -1,12 +1,13 @@ -diff --git a/src/pyscenic/prune.py b/src/pyscenic/prune.py -index abcdef1..1234567 100644 ---- a/src/pyscenic/prune.py -+++ b/src/pyscenic/prune.py -@@ -1,6 +1,6 @@ - +--- pyscenic-0.12.1/src/pyscenic/prune.py.orig 2022-11-21 10:38:05.000000000 +0000 ++++ pyscenic-0.12.1/src/pyscenic/prune.py 2024-10-02 10:20:58.423708208 +0000 +@@ -20,8 +20,8 @@ + from dask import delayed + from dask.dataframe import from_delayed + from dask.distributed import Client, LocalCluster -from multiprocessing_on_dill.connection import Pipe -from multiprocessing_on_dill.context import Process -+from multiprocessing.connection import Pipe ++from multiprocessing import Pipe +from multiprocessing import Process - - + + from .log import create_logging_handler + from .transform import ( From e84caeb29bd92ab4858413f2fbe29726d6d692de Mon Sep 17 00:00:00 2001 From: LiliyaBioinf Date: Wed, 2 Oct 2024 13:13:59 +0200 Subject: [PATCH 67/69] Update dill_patch.patch --- recipes/pyscenic/dill_patch.patch | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/recipes/pyscenic/dill_patch.patch b/recipes/pyscenic/dill_patch.patch index d94a8d43e4191..a01549df70c8c 100644 --- a/recipes/pyscenic/dill_patch.patch +++ b/recipes/pyscenic/dill_patch.patch @@ -1,4 +1,4 @@ ---- pyscenic-0.12.1/src/pyscenic/prune.py.orig 2022-11-21 10:38:05.000000000 +0000 +--- pyscenic-0.12.1/src/pyscenic/prune.py 2022-11-21 10:38:05.000000000 +0000 +++ pyscenic-0.12.1/src/pyscenic/prune.py 2024-10-02 10:20:58.423708208 +0000 @@ -20,8 +20,8 @@ from dask import delayed @@ -9,5 +9,3 @@ +from multiprocessing import Pipe +from multiprocessing import Process - from .log import create_logging_handler - from .transform import ( From 1264133be2aa9add40bf3b54937b09aeba826a7d Mon Sep 17 00:00:00 2001 From: mencian Date: Thu, 3 Oct 2024 15:08:36 -0500 Subject: [PATCH 68/69] clean up recipe, pin python to >=3.6 --- recipes/pyscenic/meta.yaml | 152 +++++++++++++++++++------------------ 1 file changed, 79 insertions(+), 73 deletions(-) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 911e84232d8a5..5cb971112ce31 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -1,73 +1,79 @@ -{% set name = "pyscenic" %} -{% set version = "0.12.1" %} -{% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} - -package: - name: "{{ name|lower }}" - version: "{{ version }}" - -source: - url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: "{{ sha256 }}" - patches: - - dill_patch.patch - -build: - number: 0 - noarch: python - run_exports: - - "{{ pin_subpackage(name, max_pin='x.x') }}" - script: "{{ PYTHON }} -m pip install . -vv" - -requirements: - build: - - python >=3.10,<3.11 - - pip - - setuptools - - wheel - - host: - - python >=3.10,<3.11 - - pip - - setuptools - - wheel - - run: - - python >=3.10,<3.11 - - aiohttp - - arboreto - - attrs - - boltons - - cloudpickle - - cytoolz - - dill - - dask >=2023.4.1 - - distributed >=2023.4.1,<2023.5.0 - - frozendict - - fsspec - - llvmlite - - loompy - - networkx - - numba >=0.51.2 - - numexpr - - pandas >=1.3.5 - - pyyaml - - requests - - scikit-learn - - scipy - - tqdm - - umap-learn - - numpy ==1.23.5 - - pyarrow - - interlap - - ctxcore - -test: - imports: - - pyscenic - -about: - home: https://github.com/aertslab/pySCENIC - summary: 'pySCENIC is a python implementation of the SCENIC pipeline' - license: MIT - license_family: MIT +{% set name = "pyscenic" %} +{% set version = "0.12.1" %} +{% set sha256 = "ae8fafa707d2578ffe08f9eed85f14a4cd9e1b53d57217420e2e956f0a8ddba2" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" + sha256: "{{ sha256 }}" + patches: + - dill_patch.patch + +build: + number: 0 + noarch: python + entry_points: + - pyscenic = pyscenic.cli.pyscenic:main + - db2feather = pyscenic.cli.db2feather:main + - csv2loom = pyscenic.cli.csv2loom:main + - invertdb = pyscenic.cli.invertdb:main + - gmt2regions = pyscenic.cli.gmt2regions:main + run_exports: + - "{{ pin_subpackage(name, max_pin='x.x') }}" + script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv" + +requirements: + host: + - python >=3.6 + - pip + run: + - python >=3.6 + - aiohttp + - arboreto + - attrs + - boltons + - cloudpickle + - cytoolz + - dill + - dask-core >=2023.4.1 + - distributed >=2023.4.1,<2023.5.0 + - frozendict + - fsspec + - llvmlite + - loompy + - networkx + - numba >=0.51.2 + - numexpr + - pandas >=1.3.5 + - pyyaml + - requests + - scikit-learn + - scipy + - tqdm + - umap-learn + - numpy ==1.23.5 + - pyarrow + - interlap + - ctxcore + +test: + imports: + - pyscenic + +about: + home: "https://github.com/aertslab/pySCENIC" + summary: "Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments." + license: "GPL-3.0-or-later" + license_family: GPL3 + license_file: "LICENSE.txt" + dev_url: "https://github.com/aertslab/pySCENIC" + doc_url: "https://scenic.aertslab.org" + +extra: + identifiers: + - doi:10.1038/nmeth.4463 + - doi:10.1038/s41592-023-01938-4 + - biotools:scenic From 9940869d82fcabef43e7a03d40a96a2befa609a2 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 29 Oct 2024 10:44:06 -0500 Subject: [PATCH 69/69] Update meta.yaml --- recipes/pyscenic/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/pyscenic/meta.yaml b/recipes/pyscenic/meta.yaml index 5cb971112ce31..dfbec6edf7f79 100644 --- a/recipes/pyscenic/meta.yaml +++ b/recipes/pyscenic/meta.yaml @@ -29,6 +29,7 @@ requirements: host: - python >=3.6 - pip + - setuptools run: - python >=3.6 - aiohttp