diff --git a/.github/renovate.json b/.github/renovate.json index c54154b..0b3e5d8 100644 --- a/.github/renovate.json +++ b/.github/renovate.json @@ -5,7 +5,7 @@ "helpers:pinGitHubActionDigestsToSemver" ], "timezone": "Europe/London", - "schedule": ["after 9am and before 5pm every weekday"], + "schedule": ["after 5am and before 5pm every weekday"], "dependencyDashboard": true, "assignees": ["jimboid"], "minimumReleaseAge": "3 days", @@ -15,5 +15,34 @@ "groupName": "GitHub Actions", "addLabels": ["ci", "dependencies"] } + ], + "customManagers": [ + { + "customType": "regex", + "managerFilePatterns": [ + "/(^|/)Dockerfile[^/]*$/" + ], + "matchStringsStrategy": "recursive", + "matchStrings": [ + "pip3? install[\\s\\S]*?(?(?:[\\w.-]+==[\\w.-]+[\\s\\\\]*)+)", + "(?[\\w.-]+)==(?[\\w.-]+)" + ], + "datasourceTemplate": "pypi", + "versioningTemplate": "pep440" + }, + { + "customType": "regex", + "managerFilePatterns": [ + "/(^|/)Dockerfile[^/]*$/" + ], + "matchStringsStrategy": "recursive", + "matchStrings": [ + "(?:mamba|conda) install[\\s\\S]*?(?(?:(?:[\\w-]+::)?[\\w.-]+=[\\w.-]+[\\s\\\\]*)+)", + "(?:(?[\\w-]+)::)?(?[\\w.-]+)=(?[\\w.-]+)" + ], + "datasourceTemplate": "conda", + "registryUrlTemplate": "https://api.anaconda.org/package/{{#if channel}}{{channel}}{{else}}conda-forge{{/if}}/", + "versioningTemplate": "pep440" + } ] } diff --git a/docker/Dockerfile b/docker/Dockerfile index 2ff6760..2c62828 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -11,14 +11,27 @@ USER $NB_USER WORKDIR $HOME # Install workshop deps -RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then \ - mamba install conda-forge/linux-64::gromacs=2024.5=nompi_h5f56185_100 -y; \ - elif [ "$TARGETPLATFORM" = "linux/arm64" ]; then \ - mamba install conda-forge/linux-aarch64::gromacs=2024.5=nompi_h9afd374_100 -y; \ - fi -RUN mamba install matplotlib=3.10.6 mdanalysis=2.9.0 numpy=2.3.3 scikit-learn=1.7.2 tqdm=4.67.1 mdtraj=1.11.0 iprogress ipywidgets -y -RUN pip install alphashape==1.3.1 click==8.3.0 click-log==0.4.0 coby==1.0.9 pbr==7.0.1 rtree==1.4.1 shapely==2.1.2 trimesh==4.8.3 vermouth==0.15.0 - +RUN conda install -y -c conda-forge \ + conda-forge::matplotlib=3.10.6 \ + conda-forge::mdanalysis=2.9.0 \ + conda-forge::numpy=2.3.3 \ + conda-forge::scikit-learn=1.7.2 \ + conda-forge::tqdm=4.67.1 \ + conda-forge::mdtraj=1.11.0 \ + conda-forge::iprogress=0.4 \ + conda-forge::ipywidgets=8.1.9 \ + conda-forge::gromacs=2026.3=nompi_* +RUN pip install --no-cache-dir \ + alphashape==1.3.1 \ + click==8.3.0 \ + click-log==0.4.0 \ + coby==1.0.9 \ + pbr==7.0.1 \ + rtree==1.4.1 \ + shapely==2.1.2 \ + trimesh==4.8.3 \ + vermouth==0.15.0 + # Get workshop files and move them to jovyan directory. COPY --chown=1000:100 . . RUN rm -rf environment.yml LICENSE README.md docker .git .github