Merge pull request #23 from dwhswenson/update-miniforge

Update miniforge action

Author: dwhswenson

.github/workflows/ci.yml

@@ -21,21 +21,20 @@ jobs:
     strategy:
       matrix:
         CONDA_PY:
-          - "3.8"
-          - "3.9"
+          - "3.12"
+          - "3.11"
           - "3.10"
-          #- "3.11"
 
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.CONDA_PY }}
           environment-file: binder/environment.yml
           activate-environment: ops-tutorial
-          miniforge-variant: Mambaforge
+          miniforge-version: latest
       - name: "Install testing tools"
         run: python -m pip install pytest nbval
       - name: "Conda info"
@@ -60,21 +59,20 @@ jobs:
     strategy:
       matrix:
         CONDA_PY:
-          - "3.8"
-          - "3.9"
+          - "3.12"
+          - "3.11"
           - "3.10"
-          #- "3.11"
 
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-python@v2
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.CONDA_PY }}
           environment-file: binder/environment.yml
           activate-environment: ops-tutorial
-          miniforge-variant: Mambaforge
+          miniforge-version: latest
       - name: "Install testing tools"
         run: python -m pip install pytest nbval
       - name: "Conda info"
@@ -85,7 +83,7 @@ jobs:
         run: source devtools/patch-all
       - name: "Run tests"
         run: |
-          pytest --nbval-lax 5_custom_shooting_setup.ipynb
+          pytest -v --durations=0 --nbval-lax 5_custom_shooting_setup.ipynb
           source devtools/run5.sh
           pytest --nbval-lax \
             6_custom_shooting_analysis.ipynb \

4_mstis_sampling_tutorial.ipynb

@@ -224,6 +224,8 @@
     "    filename = \"./inputs/mstis_bootstrap_py3.nc\"\n",
     "elif (3, 8) <= sys.version_info < (3, 11):\n",
     "    filename = \"./inputs/mstis_bootstrap_py38.nc\"\n",
+    "elif (3, 11) <= sys.version_info:\n",
+    "    filename = \"./inputs/mstis_bootstrap_py311.nc\"\n",
     "else:\n",
     "    raise RuntimeError(\n",
     "        \"Uh oh! Looks like we don't have an input file for your Python version: \"\n",
@@ -613,7 +615,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.13"
+   "version": "3.11.8"
   },
   "toc": {
    "base_numbering": 1,

5_custom_shooting_setup.ipynb

@@ -52,8 +52,12 @@
     "import sys\n",
     "if sys.version_info < (3, 8):\n",
     "    f_version = \"\"\n",
+    "elif sys.version_info < (3, 11):\n",
+    "    f_version = \"_38\"\n",
+    "elif sys.version_info < (3, 12):\n",
+    "    f_version = \"_311\"\n",
     "else:\n",
-    "    f_version = \"_38\""
+    "    f_version = \"_312\""
    ]
   },
   {
@@ -425,7 +429,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -439,7 +443,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.12.8"
   },
   "toc": {
    "base_numbering": 1,

7_parallel_tis_setup.ipynb

@@ -37,8 +37,14 @@
     "import sys\n",
     "if sys.version_info < (3, 8):\n",
     "    f_version = \"\"\n",
+    "elif sys.version_info < (3, 11):\n",
+    "    f_version = \"_38\"\n",
+    "elif sys.version_info < (3, 12):\n",
+    "    f_version = \"_311\"\n",
+    "elif sys.version_info < (3, 13):\n",
+    "    f_version = \"_312\"\n",
     "else:\n",
-    "    f_version = \"_38\""
+    "    raise RuntimeError(\"Unsupported Python version\")"
    ]
   },
   {
@@ -333,7 +339,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -347,7 +353,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.12.8"
   }
  },
  "nbformat": 4,

binder/environment.yml

@@ -12,6 +12,5 @@ dependencies:
   - openpathsampling-cli
   - openmmtools
   - jupyterlab
-  - ipywidgets <8
-  - numpy <1.24
+  - mdtraj != 1.11  # formal charge error round-tripping Topology via pandas
 prefix: /Users/dwhs/miniconda3/envs/ops-tutorial