From 394cd9a769e7517efca484ccf11086167448f025 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 25 Nov 2024 07:55:11 +0000 Subject: [PATCH 1/5] Bump coverage from 7.6.4 to 7.6.8 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.6.4 to 7.6.8. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.6.4...7.6.8) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a6e44d0c3..ce57067bb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,7 +45,7 @@ dependencies = [ test = [ # Dependencies required for running the test suite "pytest==8.3.3", - "coverage==7.6.4", + "coverage==7.6.8", "pandas==2.2.3", "seaborn==0.13.2", "ete3", From 15117aebfe11ea052a09b0b3e548682ef1f1e009 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 29 Nov 2024 07:21:31 +0000 Subject: [PATCH 2/5] Bump ruff from 0.7.2 to 0.8.1 Bumps [ruff](https://github.com/astral-sh/ruff) from 0.7.2 to 0.8.1. - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](https://github.com/astral-sh/ruff/compare/0.7.2...0.8.1) --- updated-dependencies: - dependency-name: ruff dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a6e44d0c3..0561d9930 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ test = [ ] dev = [ # Dependencies required for development (linting, type checking, etc.) - "ruff==0.7.2", + "ruff==0.8.1", "mypy==1.13.0", "mypy-extensions==1.0.0", "gprof2dot==2024.6.6", From fa6077a848c53c5f7af7644b123ceb813014b290 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 2 Dec 2024 07:45:11 +0000 Subject: [PATCH 3/5] Bump matplotlib from 3.9.2 to 3.9.3 Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.9.2 to 3.9.3. - [Release notes](https://github.com/matplotlib/matplotlib/releases) - [Commits](https://github.com/matplotlib/matplotlib/compare/v3.9.2...v3.9.3) --- updated-dependencies: - dependency-name: matplotlib dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index a6e44d0c3..49c8e66e6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ dependencies = [ "pyvdrm @ git+https://github.com/cfe-lab/pyvdrm.git@v0.3.2", "numpy==2.1.3", "scipy==1.14.1", - "matplotlib==3.9.2", + "matplotlib==3.9.3", "cutadapt==4.9", "python-Levenshtein==0.26.1", "PyYAML==6.0.2", From d0440288b7ed1119f3c85fab8b5db3d2aa13bc51 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 2 Dec 2024 18:08:19 +0000 Subject: [PATCH 4/5] Bump pytest from 8.3.3 to 8.3.4 Bumps [pytest](https://github.com/pytest-dev/pytest) from 8.3.3 to 8.3.4. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/8.3.3...8.3.4) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b229e07e3..66f7c2ca8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -44,7 +44,7 @@ dependencies = [ [project.optional-dependencies] test = [ # Dependencies required for running the test suite - "pytest==8.3.3", + "pytest==8.3.4", "coverage==7.6.8", "pandas==2.2.3", "seaborn==0.13.2", From 4d0066c46a53be2749a09d49a0bc8ff1595e4d3e Mon Sep 17 00:00:00 2001 From: Vitaliy Mysak Date: Wed, 4 Dec 2024 14:31:40 -0800 Subject: [PATCH 5/5] Make docker install faster for development --- Dockerfile | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 6c65f2eb2..ef9acac73 100644 --- a/Dockerfile +++ b/Dockerfile @@ -87,13 +87,17 @@ RUN apt-get install -q -y zlib1g-dev libncurses5-dev libncursesw5-dev && \ RUN apt-get install -q -y libcairo2-dev RUN pip install --upgrade pip -COPY . /opt/micall/ - +## Install just the dependencies of MiCall (for faster build times in development). +COPY pyproject.toml README.md /opt/micall/ RUN pip install /opt/micall[denovo,basespace] -RUN micall make_blast_db ## Trigger matplotlib to build its font cache RUN python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' +COPY . /opt/micall/ + +RUN pip install /opt/micall[denovo,basespace] +RUN micall make_blast_db + WORKDIR /data ENTRYPOINT ["micall", "micall_docker"]