Merge branch 'develop' into reader_test

.codecov.yml

@@ -14,3 +14,6 @@ comment:
   paths: null
 ignore:
   - "imdclient/_version.py"
+  - "imdclient/data"
+  - "imdclient/tests"
+  - "examples"

.github/workflows/deploy.yaml

@@ -0,0 +1,149 @@
+# On PR or push to package-* branch, build wheels and src dists
+# On tag with version number, build wheels and src dists and upload to testpypi
+# On release, build wheels and src dists and upload to pypi
+
+name: Build and upload to PyPI
+
+on:
+    pull_request:
+      branches:
+        - "main"
+    push:
+      tags:
+        - "v*"
+    release:
+        types:
+            - published
+
+concurrency:
+  group: "${{ github.ref }}-${{ github.head_ref }}-${{ github.workflow }}"
+  cancel-in-progress: true
+
+
+defaults:
+  run:
+    shell: bash -l {0}
+
+
+jobs:
+  build_wheels:
+    name: Build wheels
+    if: github.repository == 'Becksteinlab/imdclient'
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel
+
+      - name: Build wheel
+        run: |
+          pip wheel --no-deps . -w wheelhouse/
+
+      - name: Print directory contents
+        run: |
+          echo "Contents of the wheelhouse directory:"
+          ls -l wheelhouse
+          
+      - name: upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifact-whl
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: build package source distribution
+    if: github.repository == 'Becksteinlab/imdclient'
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - name: Print directory contents
+        run: |
+          echo "Contents of the dist directory:"
+          ls -l dist
+
+      - name: upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifact-sdist
+          path: ./dist/*.tar.gz
+
+  upload_testpypi_imdclient:
+    name: testpypi_upload_imdclient
+    if: |
+      github.repository == 'Becksteinlab/imdclient' &&
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v'))
+    environment:
+      name: publisher
+      url: https://test.pypi.org/p/imdclient
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    needs: [build_wheels, build_sdist]
+    steps:
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact-whl
+          path: dist
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact-sdist
+          path: dist
+
+      - name: Print directory contents
+        run: |
+          echo "Contents of the dist directory:"
+          ls -l dist
+
+      - name: upload_source_and_wheels
+        uses: pypa/[email protected]
+        with:
+          skip-existing: true
+          repository-url: https://test.pypi.org/legacy/
+          verbose: true
+
+  upload_pypi_imdclient:
+    name: pypi_upload_imdclient
+    if: | 
+      github.repository == 'Becksteinlab/imdclient' &&
+      github.event_name == 'release' && github.event.action == 'published'
+    environment:
+      name: publisher
+      url: https://pypi.org/p/imdclient
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+    needs: [build_wheels, build_sdist]
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact-whl
+          path: dist
+
+      - uses: actions/download-artifact@v4
+        with:
+          name: artifact-sdist
+          path: dist
+
+      - name: Print directory contents
+        run: |
+          echo "Contents of the dist directory:"
+          ls -l dist
+
+      - name: upload_source_and_wheels
+        uses: pypa/[email protected]

.github/workflows/gh-ci.yaml

@@ -6,6 +6,7 @@ on:
   pull_request:
     branches:
       - main
+      - develop
   schedule:
     # Weekly tests at midnight on Sundays run on main by default:
     #   Scheduled workflows run on the latest commit on the default or base branch.
@@ -24,6 +25,7 @@ defaults:
 
 jobs:
   environment-config:
+    if: github.repository == 'Becksteinlab/imdclient'
     runs-on: ubuntu-latest
     outputs:
       stable-python-version: ${{ steps.get-compatible-python.outputs.stable-python }}
@@ -39,6 +41,7 @@ jobs:
           release: "latest"
 
   main-tests:
+    if: github.repository == 'Becksteinlab/imdclient'
     needs: environment-config
     runs-on: ${{ matrix.os }}
     strategy:
@@ -100,10 +103,13 @@ jobs:
         conda info
         conda list
 
-
-    - name: Run tests
+    - name: Run IMDClient tests
       run: |
         pytest -n auto -v --cov=imdclient --cov-report=xml --color=yes imdclient/tests/test_imdclient.py
+  
+    - name: Run IMDReader tests
+      run: |
+        pytest -n auto -v --cov=imdclient --cov-report=xml --color=yes imdclient/tests/test_imdreader.py
 
     - name: codecov
       if: github.event_name != 'schedule'
@@ -113,7 +119,67 @@ jobs:
         name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
         verbose: True
 
+  simulation_engine_tests:
+    if: github.repository == 'Becksteinlab/imdclient'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build information
+        run: |
+          uname -a
+          df -h
+          ulimit -a
+
+      - name: Install conda dependencies
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: "3.11"
+          environment-file: devtools/conda-envs/test_env.yaml
+          add-pip-as-python-dependency: true
+          architecture: x64
+
+          channels: conda-forge, defaults
+
+          activate-environment: imdclient-test
+          auto-update-conda: true
+          auto-activate-base: false
+          show-channel-urls: true
+          miniconda-version: latest
+
+      - name: Install MDAnalysis version
+        uses: MDAnalysis/install-mdanalysis@main
+        with:
+          version: latest
+          install-tests: true
+          installer: conda
+          shell: bash -l {0} 
+
+      - name: Install package
+        run: |
+          python --version
+          python -m pip install .  --no-deps 
+
+      - name: Pull container
+        run: |
+          docker pull ghcr.io/becksteinlab/streaming-md-docker:main-Common-CPU
+
+      - name: Run GROMACS tests
+        run: |
+          pytest -v --color=yes imdclient/tests/test_gromacs.py
+    
+      - name: Run LAMMPS tests
+        run: |
+          pytest -v --color=yes imdclient/tests/test_lammps.py
+  
+      # SUSPEND until NAMD permissions are resolved
+      # - name: Run NAMD tests
+      #   run: |
+      #     pytest -v --color=yes imdclient/tests/test_namd.py
+
   pylint_check:
+    if: github.repository == 'Becksteinlab/imdclient'
     needs: environment-config
     runs-on: ubuntu-latest
 
@@ -139,6 +205,7 @@ jobs:
 
 
   pypi_check:
+    if: github.repository == 'Becksteinlab/imdclient'
     needs: environment-config
     runs-on: ubuntu-latest