Merge pull request #252 from VlachosGroup/mac-install-test-dev

Optional `mordred` Install Cleanup and Documentation

.github/workflows/mordred_check.yml

@@ -0,0 +1,34 @@
+name: Test mordred Install
+on:
+  schedule:
+    - cron:  '0 8 * * 1-5'
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+  workflow_dispatch:
+
+jobs:
+  optional:
+    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 mordred Install and Tests
+        run: |
+          python -m pip install -e .[mordred]
+          python -m unittest -v

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
 

aimsim/__init__.py

@@ -3,4 +3,4 @@
 from . import chemical_datastructures
 from . import utils
 
-__version__ = "2.0.1"
+__version__ = "2.0.2"

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,

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.

setup.py

@@ -41,6 +41,7 @@ def get_version(rel_path):
         "mordred": [
             "mordred==1.2.0",
             "networkx==2.*",
+            "openpyxl",
         ],
     },
     packages=find_packages(),