Merge branch 'resume-afe' of github.com:OpenFreeEnergy/openfe into resume-afe

Author: IAlibay

.github/workflows/conda_cron.yaml

@@ -40,9 +40,9 @@ jobs:
         id: latest-version
         working-directory: openfe_repo
         run: |
-          LATEST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
-          # slice off the v, ie v0.7.2 -> 0.7.2
-          VERSION=${LATEST_TAG:1}
+          REPO="${{ github.repository }}"
+          VERSION=$(curl -s -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+            "https://api.github.com/repos/$REPO/releases/latest" | jq -r '.tag_name | ltrimstr("v")')
           echo $VERSION
           echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
 

.github/workflows/docker.yaml

@@ -78,11 +78,9 @@ jobs:
       - name: Get Latest Version
         id: latest-version
         run: |
-          LATEST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
-          echo $LATEST_TAG
-          echo "LATEST_TAG=$LATEST_TAG" >> $GITHUB_OUTPUT
-          # slice off the v, ie v0.7.2 -> 0.7.2
-          VERSION=${LATEST_TAG:1}
+          REPO="${{ github.repository }}"
+          VERSION=$(curl -s -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+            "https://api.github.com/repos/$REPO/releases/latest" | jq -r '.tag_name | ltrimstr("v")')
           echo $VERSION
           echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
 

.github/workflows/gen-lock-file.yaml

@@ -22,14 +22,10 @@ jobs:
     # This saves me some time since we only need the latest tag
     - name: Get latest tag
       id: latest-version
-      env:
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        REPO: ${{ github.repository }}
       run: |
-        LATEST_TAG=$(curl -s -H "Authorization: token $GH_TOKEN" \
-          https://api.github.com/repos/$REPO/tags \
-          | jq -r '.[0].name')
-        VERSION=${LATEST_TAG:1}
+        REPO="${{ github.repository }}"
+        VERSION=$(curl -s -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+          "https://api.github.com/repos/$REPO/releases/latest" | jq -r '.tag_name | ltrimstr("v")')
         echo $VERSION
         echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
 

.github/workflows/installer.yaml

@@ -25,9 +25,9 @@ jobs:
     - name: Get Latest Version
       id: latest-version
       run: |
-        LATEST_TAG=$(git describe --tags $(git rev-list --tags --max-count=1))
-        # slice off the v, ie v0.7.2 -> 0.7.2
-        VERSION=${LATEST_TAG:1}
+        REPO="${{ github.repository }}"
+        VERSION=$(curl -s -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
+          "https://api.github.com/repos/$REPO/releases/latest" | jq -r '.tag_name | ltrimstr("v")')
         echo $VERSION
         echo "VERSION=$VERSION" >> $GITHUB_OUTPUT
 

src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol_results.py

@@ -8,9 +8,9 @@
 
 import gufe
 import numpy as np
+import openmm
 import pytest
 from openff.units import unit as offunit
-import openmm
 
 import openfe
 from openfe.protocols import openmm_afe

src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol_results.py

@@ -7,9 +7,9 @@
 
 import gufe
 import numpy as np
+import openmm
 import pytest
 from openff.units import unit as offunit
-import openmm
 
 import openfe
 from openfe import ChemicalSystem, SolventComponent

src/openfe/tests/protocols/openmm_ahfe/test_ahfe_resume.py

@@ -7,18 +7,18 @@
 import shutil
 
 import gufe
-from gufe.protocols.errors import ProtocolUnitExecutionError
+import openmm
 import pytest
+from gufe.protocols.errors import ProtocolUnitExecutionError
 from numpy.testing import assert_allclose
 from openfe_analysis.utils.multistate import _determine_position_indices
 from openff.units import unit as offunit
 from openff.units.openmm import from_openmm
-import openmm
 from openmmtools.multistate import MultiStateReporter, ReplicaExchangeSampler
 
 import openfe
-from openfe.protocols import openmm_afe
 from openfe.data._registry import POOCH_CACHE
+from openfe.protocols import openmm_afe
 
 from ...conftest import HAS_INTERNET
 from .utils import _get_units
@@ -115,7 +115,9 @@ def test_vacuum_check_restart(protocol_settings, ahfe_vac_trajectory_path):
 class TestCheckpointResuming:
     @pytest.fixture()
     def protocol_dag(
-        self, protocol_settings, benzene_modifications,
+        self,
+        protocol_settings,
+        benzene_modifications,
     ):
         stateA = openfe.ChemicalSystem(
             {
@@ -160,7 +162,9 @@ def _copy_simfiles(cwd: pathlib.Path, filepath):
         shutil.copyfile(filepath, f"{cwd}/{filepath.name}")
 
     @pytest.mark.integration
-    def test_resume(self, protocol_dag, ahfe_solv_trajectory_path, ahfe_solv_checkpoint_path, tmpdir):
+    def test_resume(
+        self, protocol_dag, ahfe_solv_trajectory_path, ahfe_solv_checkpoint_path, tmpdir
+    ):
         """
         Attempt to resume a simulation unit with pre-existing checkpoint &
         trajectory files.
@@ -244,4 +248,4 @@ def test_resume(self, protocol_dag, ahfe_solv_trajectory_path, ahfe_solv_checkpo
 
         # Check the free energy plots are there
         mbar_overlap_file = cwd / "mbar_overlap_matrix.png"
-        assert (mbar_overlap_file).exists()
+        assert (mbar_overlap_file).exists()