Fixes #249, adds dependencies for PyPI packaging and updates CI tests

.github/actions/conda-setup/action.yml

@@ -47,13 +47,18 @@ runs:
     - name: Update environment
       shell: bash -l {0}
       run: |
-        if [ -f "${{ inputs.filename }}" ]; then
+        if [ -f "${{ inputs.filename }}" ] && ! [ "${{ steps.cache.outputs.cache-hit }}" ] ; then
           mamba env update -n ${{ inputs.env_name }} -f ${{ inputs.filename }}
         else
           echo "No conda environment file found; skipping. Path: ${{ inputs.filename }}"
           mamba install -n ${{ inputs.env_name }} python=${{ inputs.python-version }}
         fi
-      if: steps.cache.outputs.cache-hit != 'true'
+    - name: Install required binaries for MPI
+      shell: bash -l {0}
+      run: |
+        if ! grep -q ${{ inputs.filename }} ; then
+          sudo apt install libopenmpi-dev
+        fi
     - name: Setup the  environment
       shell: bash -l {0}
       run: |

environment.yml

@@ -14,6 +14,7 @@ dependencies:
   - ipywidgets
   - tqdm
   - orjson
+  - matplotlib
 # parallel
   - mpi4py
   - dask
@@ -24,16 +25,11 @@ dependencies:
   - jupyterlab>=3
   - jupyterlab-lsp
   - python-lsp-server
-  - matplotlib
   - pygments
   - mkdocs
   - mkdocstrings
   - mkdocs-material
-  # NOTE: we are installing mkdocs-jupyter with pip for now
-  # due to the following: https://github.com/conda-forge/mkdocs-jupyter-feedstock/issues/31
-  # - mkdocs-jupyter
+  - mkdocs-jupyter
   - mkdocstrings-python
   - ruff
   - typing-extensions
-  - pip:
-      - mkdocs-jupyter>=0.24.7

pyproject.toml

@@ -17,8 +17,17 @@ classifiers = [
   "Topic :: Scientific/Engineering",
 ]
 dependencies = [
-  # All core dependencies must be sourced from conda (conda-forge).
-  # See ``environment.yml`` for further information.
+  "deap",
+  "numpy",
+  "pydantic>=2.3",
+  "pyyaml",
+  "botorch>=0.9.2,<=0.10.0",
+  "scipy>=1.10.1",
+  "pandas",
+  "ipywidgets",
+  "tqdm",
+  "orjson",
+  "matplotlib"
 ]
 description = "Flexible optimization of arbitrary problems in Python."
 dynamic = [ "version" ]
@@ -31,6 +40,15 @@ requires-python = ">=3.9"
 dev = [
   "pytest",
   "pytest-cov",
+  "ffmpeg",
+  "pytest",
+  "pytest-cov",
+  "jupyterlab>=3",
+  "jupyterlab-lsp",
+  "python-lsp-server",
+  "pygments",
+  "dask",
+  "mpi4py"
 ]
 doc = [
   "mkdocs",