refactoring shortcut.py

.github/workflows/build.yml

@@ -29,7 +29,6 @@ jobs:
         python3-setuptools
         python3-numpy
         python3-pil
-        python3-pytest
         python3-pip
 
     - name: Install collada2gltf
@@ -45,13 +44,14 @@ jobs:
     - name: Build
       run: |
         pip install --upgrade pip
-        pip install -v --config-settings testing=True .
+        pip install -v --config-settings testing=True .[dev]
       env:
         DEBUG: 1
 
     - name: Test
       run: |
         pymol -ckqy testing/testing.py --run all
+        python -m pytest tests -vv
 
   build-Windows:
 
@@ -74,7 +74,7 @@ jobs:
       shell: cmd
       run: |-
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest pip python-build
+        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pip python-build
 
     - name: Conda info
       shell: cmd
@@ -94,13 +94,14 @@ jobs:
       shell: cmd
       run: |
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
-        pip install -v --config-settings testing=True .
+        pip install -v --config-settings testing=True .[dev]
 
     - name: Test
       shell: cmd
       run: |
         CALL %CONDA_ROOT%\\Scripts\\activate.bat
         pymol -ckqy testing\\testing.py --run all
+        python -m pytest tests -vv
 
   build-MacOS:
 
@@ -117,7 +118,7 @@ jobs:
         bash $CONDA_ROOT.sh -b -p $CONDA_ROOT
         export PATH="$CONDA_ROOT/bin:$PATH"
         conda config --set quiet yes
-        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pytest pip python-build
+        conda install -y -c conda-forge -c schrodinger python cmake libpng freetype pyside6 glew libxml2 numpy=1.26.4 catch2=2.13.3 glm libnetcdf collada2gltf biopython pillow msgpack-python pip python-build
         conda info
 
     - name: Get additional sources
@@ -131,9 +132,10 @@ jobs:
       run: |-
         export MACOSX_DEPLOYMENT_TARGET=12.0
         export PATH="$CONDA_ROOT/bin:$PATH"
-        pip install -v --config-settings testing=True .
+        pip install -v --config-settings testing=True .[dev]
 
     - name: Test
       run: |-
         export PATH="$CONDA_ROOT/bin:$PATH"
         pymol -ckqy testing/testing.py --run all
+        python -m pytest tests -vv

modules/pymol.egg-info/PKG-INFO

@@ -0,0 +1,94 @@
+Metadata-Version: 2.1
+Name: pymol
+Version: 3.1.0a0
+Summary: PyMOL is a Python-enhanced molecular graphics tool.
+Author-email: Schrodinger <pymol-users@lists.sourceforge.net>
+License: 
+         Open-Source PyMOL Copyright Notice
+         ==================================
+
+         The Open-Source PyMOL source code is copyrighted, but you can freely
+         use and copy it as long as you don't change or remove any of the
+         Copyright notices. The Open-Source PyMOL product is made available
+         under the following open-source license terms:
+
+         ----------------------------------------------------------------------
+         Open-Source PyMOL is Copyright (C) Schrodinger, LLC.
+
+         All Rights Reserved
+
+         Permission to use, copy, modify, distribute, and distribute modified
+         versions of this software and its built-in documentation for any
+         purpose and without fee is hereby granted, provided that the above
+         copyright notice appears in all copies and that both the copyright
+         notice and this permission notice appear in supporting documentation,
+         and that the name of Schrodinger, LLC not be used in advertising or
+         publicity pertaining to distribution of the software without specific,
+         written prior permission.
+
+         SCHRODINGER, LLC DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
+         INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN
+         NO EVENT SHALL SCHRODINGER, LLC BE LIABLE FOR ANY SPECIAL, INDIRECT OR
+         CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+         OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+         OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE
+         USE OR PERFORMANCE OF THIS SOFTWARE.
+         ----------------------------------------------------------------------
+
+         PyMOL Trademark Notice
+         ======================
+
+         PyMOL(TM) is a trademark of Schrodinger, LLC. Derivative
+         software which contains PyMOL source code must be plainly
+         distinguished from any and all PyMOL products distributed by Schrodinger,
+         LLC in all publicity, advertising, and documentation.
+
+         The slogans, "Includes PyMOL(TM).", "Based on PyMOL(TM) technology.",
+         "Contains PyMOL(TM) source code.", and "Built using PyMOL(TM).", may
+         be used in advertising, publicity, and documentation of derivative
+         software provided that the notice, "PyMOL is a trademark of Schrodinger,
+         LLC.", is included in a footnote or at the end of the
+         document.
+
+         All other endorsements employing the PyMOL trademark require specific,
+         written prior permission.
+
+
+Project-URL: Homepage, https://pymol.org
+Project-URL: Documentation, https://pymol.org/dokuwiki
+Project-URL: Repository, https://github.com/schrodinger/pymol-open-source
+Project-URL: Bug Tracker, https://github.com/schrodinger/pymol-open-source/issues
+Project-URL: Changelog, https://github.com/schrodinger/pymol-open-source/blob/master/ChangeLog
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS
+Requires-Dist: numpy<2,>=1.26.4
+Provides-Extra: dev
+Requires-Dist: numpy<2,>=1.26.4; extra == "dev"
+Requires-Dist: pillow==10.3.0; extra == "dev"
+Requires-Dist: pytest==8.2.2; extra == "dev"
+
+[![CI](https://github.com/schrodinger/pymol-open-source/workflows/CI/badge.svg)](https://github.com/schrodinger/pymol-open-source/actions)
+
+<img src="./data/pymol/icons/icon2.svg" height="100" align="right" />
+
+# Open-Source PyMOL
+
+[Open-source foundation](https://pymol.org/#opensource) of the user-sponsored PyMOL molecular visualization system.
+
+The commercial PyMOL product ("Incentive PyMOL") with maintenance and support is available from https://pymol.org
+
+## Installation
+
+See [INSTALL](INSTALL).
+
+## Contributing
+
+See [DEVELOPERS](DEVELOPERS).
+
+## License
+
+Copyright (c) [Schrodinger, LLC](https://www.schrodinger.com/)
+
+Published under a BSD-like license, see [LICENSE](LICENSE).