Fix old showcase for 1.0 release

.binder/environment.yml

@@ -28,5 +28,5 @@ dependencies:
   - rdkit
   - typing_extensions
   - gufe>=0.9.4
-  - openfe>=0.13.0
+  - openfe~=1.0
   - py3dmol

.github/workflows/CI.yml

@@ -4,11 +4,9 @@ on:
   push:
     branches:
       - main
-      - master
   pull_request:
     branches:
       - main
-      - master
   schedule:
     # nightly tests, 2 am
     - cron: "0 2 * * *"
@@ -23,7 +21,7 @@ concurrency:
 
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash -leo pipefail {0}
 
 jobs:
   test:
@@ -36,18 +34,21 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2.4.0
+
+    - name: Get current date
+      id: date
+      run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}"
 
-    - uses: conda-incubator/setup-miniconda@v2.1.1
+    - uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: "${{ matrix.python-version }}"
         environment-file: .binder/environment.yml
-        activate-environment: test
-        auto-activate-base: false
-        mamba-version: "*"
-        miniforge-version: latest
-        miniforge-variant: Mambaforge
-        use-mamba: true
-        channel-priority: true
+        cache-environment: true
+        cache-downloads: true
+        cache-environment-key: environment-${{ steps.date.outputs.date }}
+        cache-downloads-key: downloads-${{ steps.date.outputs.date }}
+        create-args: >-
+          python=${{ matrix.python-version }}
+        init-shell: bash
 
     - name: Additional info about the build
       run: |

networks/ligand_networks_for_developers.ipynb

@@ -145,6 +145,19 @@
     "        super().__init__()\n",
     "        self.remove_middle = remove_middle\n",
     "    \n",
+    "    @classmethod\n",
+    "    def _defaults(cls):\n",
+    "        return {}\n",
+    "    \n",
+    "    def _to_dict(self) -> dict:\n",
+    "        # a dict with enough information to reconstruct this object\n",
+    "        return {'remove_middle': self.remove_middle}\n",
+    "    \n",
+    "    @classmethod\n",
+    "    def _from_dict(cls, dct: dict):\n",
+    "        # reconstruct a mapper from previously being serialised\n",
+    "        return cls(dct['remove_middle'])\n",
+    "    \n",
     "    def _mappings_generator(self, componentA, componentB):\n",
     "        try:\n",
     "            return [my_mapping_function(componentA.to_rdkit(),\n",
@@ -284,6 +297,17 @@
    "outputs": [],
    "source": [
     "class MultiMapper(LigandAtomMapper):\n",
+    "    @classmethod\n",
+    "    def _defaults(cls):\n",
+    "        return {}\n",
+    "    \n",
+    "    def _to_dict(self) -> dict:\n",
+    "        return {}\n",
+    "    \n",
+    "    @classmethod\n",
+    "    def _from_dict(cls, dct: dict):\n",
+    "        return cls()\n",
+    "        \n",
     "    def _mappings_generator(self, componentA, componentB):\n",
     "        mappings = []\n",
     "        for remove_middle in [True, False]:\n",
@@ -383,6 +407,17 @@
    "outputs": [],
    "source": [
     "class GeneratorMapper(LigandAtomMapper):\n",
+    "    @classmethod\n",
+    "    def _defaults(cls):\n",
+    "        return {}\n",
+    "    \n",
+    "    def _to_dict(self) -> dict:\n",
+    "        return {}\n",
+    "    \n",
+    "    @classmethod\n",
+    "    def _from_dict(cls, dct: dict):\n",
+    "        return cls()\n",
+    "        \n",
     "    def _mappings_generator(self, componentA, componentB):\n",
     "        for remove_middle in [True, False]:\n",
     "            try:\n",
@@ -996,7 +1031,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

openmm_rbfe/benchmark_demo.ipynb

@@ -318,7 +318,8 @@
     "# tweak to hearts content\n",
     "settings.simulation_settings.equilibration_length = 6 * unit.picosecond\n",
     "settings.simulation_settings.production_length = 6 * unit.picosecond\n",
-    "settings.alchemical_sampler_settings.n_repeats = 1  # number of completely independent runs, variance is std of means of these\n",
+    "settings.protocol_repeats = 1  # number of completely independent runs, variance is std of means of these\n",
+    "\n",
     "\n",
     "# put Settings into Protocol\n",
     "# the settings are now \"locked in\"/read-only and can't be further modified\n",
@@ -480,7 +481,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.10"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,