From 0fd6abae5895872cc671342a4e9f9d1610138308 Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 21:11:38 -0500
Subject: [PATCH 1/9] Create mordred_check.yml

---
 .github/workflows/mordred_check.yml | 33 +++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 .github/workflows/mordred_check.yml

diff --git a/.github/workflows/mordred_check.yml b/.github/workflows/mordred_check.yml
new file mode 100644
index 00000000..0be51044
--- /dev/null
+++ b/.github/workflows/mordred_check.yml
@@ -0,0 +1,33 @@
+name: Test mordred Install
+on:
+  schedule:
+    - cron:  '0 8 * * 1-5'
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:      
+      fail-fast: false
+      matrix:
+        python-version: '3.8'
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -el {0}
+    name: ${{ matrix.os }} Python ${{ matrix.python-version }} Subtest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+      - name: Attempt Live Install
+        run: |
+          python -m pip install aimsim[mordred]

From 48c2db069a0a5eea5fa3c6496f8bb8392e9c8efb Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 21:15:43 -0500
Subject: [PATCH 2/9] syntax error in workflow file

---
 .github/workflows/mordred_check.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/mordred_check.yml b/.github/workflows/mordred_check.yml
index 0be51044..daa24bb4 100644
--- a/.github/workflows/mordred_check.yml
+++ b/.github/workflows/mordred_check.yml
@@ -14,7 +14,7 @@ jobs:
     strategy:      
       fail-fast: false
       matrix:
-        python-version: '3.8'
+        python-version: ['3.8']
         os: [ubuntu-latest, windows-latest, macos-latest]
 
     runs-on: ${{ matrix.os }}

From a8b6563097f86106c491004d9f36f7ae7f8ad385 Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 21:51:38 -0500
Subject: [PATCH 3/9] also run tests on mordred install

---
 .github/workflows/mordred_check.yml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/mordred_check.yml b/.github/workflows/mordred_check.yml
index daa24bb4..0ef68a47 100644
--- a/.github/workflows/mordred_check.yml
+++ b/.github/workflows/mordred_check.yml
@@ -10,7 +10,7 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  optional:
     strategy:      
       fail-fast: false
       matrix:
@@ -28,6 +28,7 @@ jobs:
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-      - name: Attempt Live Install
+      - name: Attempt mordred Install and Tests
         run: |
-          python -m pip install aimsim[mordred]
+          python -m pip install -e .[mordred]
+          coverage run --source=. --omit=interfaces/*,aimsim/__main__.py,aimsim/tasks/__init__.py,aimsim/ops/__init__.py,aimsim/chemical_datastructures/__init__.py,aimsim/utils/__init__.py,setup.py,tests/*,aimsim/__init__.py,aimsim/utils/plotting_scripts.py -m unittest discover

From 6f18e0544ac02e79455e567c0502080853e79eac Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 21:51:47 -0500
Subject: [PATCH 4/9] add import back to descriptor

---
 aimsim/ops/descriptor.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/aimsim/ops/descriptor.py b/aimsim/ops/descriptor.py
index f369ff29..283701a6 100644
--- a/aimsim/ops/descriptor.py
+++ b/aimsim/ops/descriptor.py
@@ -12,6 +12,11 @@
 from padelpy import from_smiles
 from aimsim.utils.extras import requires_mordred
 
+try:
+    from mordred import Calculator, descriptors
+except ImportError:
+    NO_MORDRED = True
+
 
 from ..exceptions import (
     InvalidConfigurationError,

From 231dccbea9ee42613c2414f86538879fc6b696bb Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 21:52:05 -0500
Subject: [PATCH 5/9] fix mordred_requires decorator

---
 aimsim/utils/extras.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/aimsim/utils/extras.py b/aimsim/utils/extras.py
index 49dd7f3a..3e4fe315 100644
--- a/aimsim/utils/extras.py
+++ b/aimsim/utils/extras.py
@@ -7,7 +7,7 @@ def requires_mordred(function):
     try:
         from mordred import Calculator, descriptors
 
-        return function()
+        return function
     except ImportError:
         return MordredNotInstalledWarning(
             """Attempting to call this function ({:s}) requires mordred to be installed.

From 4200420dc53cb8b233d263bad7f8ea29e9c7616a Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 21:52:19 -0500
Subject: [PATCH 6/9] Update README.md

 - add mordred disclaimer
 - fix install instructions for zsh issues
---
 README.md | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 3370caa8..de933a72 100644
--- a/README.md
+++ b/README.md
@@ -51,7 +51,9 @@ Many of the substrates appear similar to one another and thereby redundant, but
 `pip install aimsim`
 This command also installs the required dependencies. It is recommended to install `AIMSim` in a separate virtual environment.
 
-_Optional:_ AIMSim can also use descriptors provided in the `mordred` package, but because it is an older package it is only compatible with Python 3.8. To install with `mordred` support, use `pip install aimsim[mordred]`
+_Optional:_ Previous versions of AIMSim provided direct support for the descriptors provided in the `mordred` package. Unforunately, `mordred` is no longer recieving updates and causes significant depdendency conflicts. Because of this, it is an _optional_ add-on to `AIMSim` that is only compatible with Python 3.8. To install with `mordred` support, use `pip install 'aimsim[mordred]'` (note the single quotes, necessary in `zsh`).
+
+Unit tests from previous versions of `AIMSim` have been kept but are not actively maintained due to the limitations above. Use `mordred` at your own risk.
 
 ## Running AIMSim
 `AIMSim` is compatible with Python 3.7 to 3.9.
@@ -68,9 +70,12 @@ Start `AIMSim` with a prepared configuration YAML file (`config.yaml`):
 1. Morgan Fingerprint (Equivalent to the ECFP fingerprints)
 2. RDKit Topological Fingerprint
 3. RDKit Daylight Fingerprint
+
+_The following are available via command line use (config.yaml) only:_
+
 4. All fingerprints available from the [ccbmlib](https://github.com/vogt-m/ccbmlib) package (_specify 'ccbmlib:descriptorname' for command line input_).
-5. All descriptors available through the [Mordred](https://github.com/mordred-descriptor/mordred) library (_specify 'mordred:desciptorname' for command line input._). To enable this option, you must install with `pip install aimsim['mordred']`.
-6. All descriptors and fingerprints available from [PaDELPy](https://github.com/ecrl/padelpy), an interface to PaDEL-Descriptor. (_specify 'padelpy:desciptorname' for command line input._).
+5. All descriptors and fingerprints available from [PaDELPy](https://github.com/ecrl/padelpy), an interface to PaDEL-Descriptor. (_specify 'padelpy:desciptorname' for command line input._).
+6. All descriptors available through the [Mordred](https://github.com/mordred-descriptor/mordred) library (_specify 'mordred:desciptorname' for command line input._). To enable this option, you must install with `pip install 'aimsim[mordred]'` (see disclaimer in the Installation section above).
 
 ### Currently Implemented Similarity Scores
 

From 9af6d0793141f9685efd4a2556835bab2b560e7c Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 21:54:15 -0500
Subject: [PATCH 7/9] switch test runner to default unittest

---
 .github/workflows/mordred_check.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/mordred_check.yml b/.github/workflows/mordred_check.yml
index 0ef68a47..50ad6eef 100644
--- a/.github/workflows/mordred_check.yml
+++ b/.github/workflows/mordred_check.yml
@@ -31,4 +31,4 @@ jobs:
       - name: Attempt mordred Install and Tests
         run: |
           python -m pip install -e .[mordred]
-          coverage run --source=. --omit=interfaces/*,aimsim/__main__.py,aimsim/tasks/__init__.py,aimsim/ops/__init__.py,aimsim/chemical_datastructures/__init__.py,aimsim/utils/__init__.py,setup.py,tests/*,aimsim/__init__.py,aimsim/utils/plotting_scripts.py -m unittest discover
+          python -m unittest -v
\ No newline at end of file

From 439069cf7a19495be7cce0cea0ea6d84bf3b896b Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 22:08:22 -0500
Subject: [PATCH 8/9] mordred install requires openpyxl

this is due to some version conflict, i think pandas stopped using this in later versions but because of the restrictions imposed by mordred we fall back to this
---
 setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.py b/setup.py
index 3276d0ff..19d3ab84 100644
--- a/setup.py
+++ b/setup.py
@@ -41,6 +41,7 @@ def get_version(rel_path):
         "mordred": [
             "mordred==1.2.0",
             "networkx==2.*",
+            "openpyxl",
         ],
     },
     packages=find_packages(),

From 305154f458ab8233125aca6ea472dafce117bd68 Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 22 Feb 2023 22:12:51 -0500
Subject: [PATCH 9/9] bump minor version

---
 aimsim/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/aimsim/__init__.py b/aimsim/__init__.py
index 9ef55638..cb1cb3bd 100644
--- a/aimsim/__init__.py
+++ b/aimsim/__init__.py
@@ -3,4 +3,4 @@
 from . import chemical_datastructures
 from . import utils
 
-__version__ = "2.0.1"
+__version__ = "2.0.2"