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/.github/workflows/build.yaml b/.github/workflows/build.yaml index 0596bd1..7502327 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -13,7 +13,6 @@ jobs: matrix: platform: - linux/amd64 - - linux/arm64 runs-on: ${{ matrix.platform == 'linux/amd64' && 'ubuntu-24.04' || matrix.platform == 'linux/arm64' && 'ubuntu-24.04-arm' }} name: build ${{ matrix.platform }} outputs: diff --git a/docker/Dockerfile b/docker/Dockerfile index a031257..ceea56f 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -11,7 +11,13 @@ USER $NB_USER WORKDIR $HOME # Install workshop deps -RUN mamba install -c conda-forge bioconda::blast openmm numpy=2.2 matplotlib scipy ambertools=$AMBERTOOLS_VER +RUN conda install -y -c conda-forge -c bioconda \ + conda-forge::matplotlib=3.11.1 \ + conda-forge::numpy=2.5.3 \ + conda-forge::openmm=8.6.1 \ + conda-forge::scipy=1.18.1 \ + conda-forge::ambertools=$AMBERTOOLS_VER \ + bioconda::blast=2.17.0 RUN pip install git+https://github.com/CharlieLaughton/Alphafix.git RUN mkdir blastp