Merge pull request #241 from VlachosGroup/numpy-arm-fix

Loosen Dependency Requirements for Python Compatibility by Dropping Mordred

.github/workflows/run_tests.yml

@@ -1,7 +1,6 @@
 name: Run Tests
 on:
   schedule:
-    # * is a special character in YAML so you have to quote this string
     - cron:  '0 8 * * 1-5'
   push:
     branches: [ master ]
@@ -12,24 +11,25 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
     strategy:      
       fail-fast: false
       matrix:
-        python-version: ['3.7', '3.8', '3.9']
-    name: Python ${{ matrix.python-version }} sample
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
+        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@v2      
-      - name: Setup python
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
         with:
+          auto-update-conda: true
           python-version: ${{ matrix.python-version }}
-          architecture: x64
       - name: Install Dependencies
         run: |
-          sudo apt-get install -y idle3 python3-tk
-          python -m pip install rdkit-pypi
-          python -m pip install networkx==2.1
           python -m pip install openpyxl
           python -m pip install -r requirements.txt
           python -m pip install -e .

README.md

@@ -50,6 +50,8 @@ 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]`
+
 ## Running AIMSim
 `AIMSim` is compatible with Python 3.7 to 3.9.
 Start `AIMSim` with a graphical user interface:
@@ -66,7 +68,7 @@ Start `AIMSim` with a prepared configuration YAML file (`config.yaml`):
 2. RDKit Topological Fingerprint
 3. RDKit Daylight Fingerprint
 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._).
+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._).
 
 ### Currently Implemented Similarity Scores

aimsim/__init__.py

@@ -3,4 +3,4 @@
 from . import chemical_datastructures
 from . import utils
 
-__version__ = "1.1.2"
+__version__ = "2.0.1"

aimsim/exceptions.py

@@ -14,6 +14,14 @@ def __init__(self, message=None):
         super().__init__(message)
 
 
+class MordredNotInstalledWarning(RuntimeWarning):
+    """Used in descriptor.py when the Mordred property calculator is not present."""
+
+    def __init__(self, message=None):
+        self.message = message
+        super().__init__(message)
+
+
 class InvalidConfigurationError(IOError):
     """Used when a configuration parameter is invalid."""