diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index c24cc847..55ab4477 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -14,6 +14,9 @@ on: env: PARTICIPANT_DATA: + REGISTRY: ghcr.io + ORG: nbisweden + IMAGE: workshop-pgip/workshop-pgip:latest jobs: build: @@ -26,6 +29,13 @@ jobs: run: shell: bash -l {0} steps: + - name: Set time zone + uses: szenius/set-timezone@v1.0 + with: + timezoneLinux: "Europe/Stockholm" + timezoneMacos: "Europe/Stockholm" + timezoneWindows: "W. Europe Standard Time" + - name: Cancel Previous Runs if: ${{ !env.ACT }} uses: styfle/cancel-workflow-action@0.11.0 @@ -35,24 +45,26 @@ jobs: - name: Checkout repository uses: actions/checkout@v4 - - name: Install micromamba - uses: mamba-org/setup-micromamba@v1 - with: - micromamba-version: "1.3.1-0" - environment-file: conda-linux-64.lock - environment-name: pgip - init-shell: bash - cache-environment: true - - - name: Test git installation - run: | - git --help - echo Listing branches - git branch -l - echo Fetching branches - git fetch --all - echo Listing branches again - git branch --list + - name: Pull image + run: docker pull ${{ env.REGISTRY }}/${{ env.ORG }}/${{ env.IMAGE }} + # - name: Install micromamba + # uses: mamba-org/setup-micromamba@v1 + # with: + # micromamba-version: "1.3.1-0" + # environment-file: conda-linux-64.lock + # environment-name: pgip + # init-shell: bash + # cache-environment: true + + # - name: Test git installation + # run: | + # git --help + # echo Listing branches + # git branch -l + # echo Fetching branches + # git fetch --all + # echo Listing branches again + # git branch --list - name: Install pgip dependencies run: | @@ -121,13 +133,27 @@ jobs: fi - name: Render tag and save rendered state in separate branch - uses: quarto-dev/quarto-actions/publish@v2 if: startsWith(github.ref, 'refs/tags/v') - with: - target: "archive-${{ github.ref_name }}" - path: docs env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_EMAIL: do_not_email@example.com + GITHUB_USERNAME: gh_action + TARGET: "archive-${{ github.ref_name }}" + run: | + # Add git info + git config --global user.email "${{ env.GITHUB_EMAIL }}" + git config --global user.name "${{ env.GITHUB_USERNAME }}" + git clone --single-branch --branch ${{ env.TARGET }} "https://${{ secrets.GITHUB_TOKEN }}@github.com/${GITHUB_REPOSITORY}.git" tmprepo + + + + # - name: Render tag and save rendered state in separate branch + # uses: quarto-dev/quarto-actions/publish@v2 + # if: startsWith(github.ref, 'refs/tags/v') + # with: + # target: "archive-${{ github.ref_name }}" + # path: docs + # env: + # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - name: Checkout archived course versions env: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 5613f2d1..b64fec25 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -108,3 +108,16 @@ repos: files: '(\.[rR]profile|\.R|\.Rmd|\.Rnw|\.r|\.rmd|\.rnw)$' exclude: 'renv/activate\.R' minimum_pre_commit_version: "2.13.0" + - repo: local + hooks: + - id: pylint + name: pylint + entry: pylint + language: system + types: [python] + args: + [ + "-rn", # Only display messages + "-sn", # Don't display the score + "--disable=fixme", + ] diff --git a/conda-linux-64.lock b/conda-linux-64.lock index e63b4e42..2f9fffba 100644 --- a/conda-linux-64.lock +++ b/conda-linux-64.lock @@ -1,44 +1,44 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 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+++ b/environment.yml @@ -12,13 +12,14 @@ dependencies: - bwa - ca-certificates - csvtk - - cyvcf2=0.30.16 + - cyvcf2 - demesdraw - d4tools - fastqc - gatk4 - gawk - htslib=1.15.1 + - ipykernel - jupyter - jupyter-cache - mosdepth=0.3.3 diff --git a/scripts/Dockerfile b/scripts/Dockerfile new file mode 100644 index 00000000..8f83b997 --- /dev/null +++ b/scripts/Dockerfile @@ -0,0 +1,55 @@ +# Docker file for workshop-pgip +# 2023 Per Unneberg + +FROM rocker/verse:4.2.3 +LABEL Description="Docker image for NBIS workshop Population Genomics in Practice" +LABEL Maintainer="per.unneberg@nbis.se" +LABEL org.opencontainers.image.source="https://github.com/NBISweden/workshop-pgip" +ARG QUARTO_VERSION="1.3.450" +ENV PATH="${PATH}:/miniconda3/bin" + +RUN apt-get update -y \ + && apt-get install --no-install-recommends -y \ + libxml2-dev \ + libssl-dev \ + libcurl4-openssl-dev \ + libudunits2-dev \ + libgdal-dev \ + texlive \ + texlive-latex-extra \ + && wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \ + && apt-get install -y ./google-chrome-stable_current_amd64.deb \ + && rm -rf ./google-chrome-stable_current_amd64.deb \ + && curl -o quarto-linux-amd64.deb -L https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-amd64.deb \ + && apt-get install -y ./quarto-linux-amd64.deb \ + && rm -rf ./quarto-linux-amd64.deb \ + && Rscript -e 'install.packages(c("ape", "codetools", "curl", "devtools", "dt", "dygraphs", "expm", "fontawesome", "formatr"), repos = "http://cran.us.r-project.org");' \ + && Rscript -e 'install.packages(c("formattable", "gganimate", "ggiraph", "ggraph", "ggplot2", "gifski", "gplots"), repos = "http://cran.us.r-project.org");' \ + && Rscript -e 'install.packages(c("gsalib", "highcharter", "igraph", "kableExtra", "latex2exp", "leaflet"), repos = "http://cran.us.r-project.org");' \ + && Rscript -e 'install.packages(c("networkD3", "magick", "patchwork", "pdftools", "plotly", "readr", "readxl", "reticulate"), repos = "http://cran.us.r-project.org");' \ + && Rscript -e 'install.packages(c("rmarkdown", "tidyr", "viridis"), repos = "http://cran.us.r-project.org");' \ + && rm -rf /var/lib/apt/lists/* \ + && mkdir /qmd + +RUN mkdir -p /miniconda3 \ + && wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /miniconda3/miniconda.sh \ + && bash /miniconda3/miniconda.sh -b -u -p /miniconda3 \ + && rm -rf /miniconda3/miniconda.sh + +RUN conda init bash + +COPY env.yaml /tmp/env.yaml +RUN conda env update -n base -f /tmp/env.yaml +ENV PATH /miniconda3/envs/base/bin:$PATH +RUN /bin/bash -c "source activate base" + +RUN python -m ipykernel install --user --display-name "Population Genomics in Practice (Python)" +RUN python -m pip install git+https://github.com/NBISweden/pgip-tools + +RUN Rscript -e 'install.packages("dotenv", repos=c(CRAN = "https://cran.rstudio.com/"));' \ + R -e "library(devtools); devtools::install_local('../src/R/pgip', upgrade=FALSE)" + +WORKDIR /qmd +ENV XDG_CACHE_HOME=/tmp/quarto_cache_home +ENV XDG_DATA_HOME=/tmp/quarto_data_home +CMD quarto render diff --git a/scripts/env.yaml b/scripts/env.yaml new file mode 100644 index 00000000..6a0b5c0b --- /dev/null +++ b/scripts/env.yaml @@ -0,0 +1,44 @@ +## Environment file to reproduce exercises +name: base +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bash_kernel + - bedtools + - bcftools + - bokeh + - bwa + - ca-certificates + - csvtk +# - cyvcf2 + - demesdraw + - d4tools + - fastqc + - gatk4 + - gawk +# - htslib=1.15.1 + - ipykernel + - jupyter + - jupyter-cache + - mosdepth # =0.3.3 + - msprime>=1.2 + - multiqc + - pandas + - pip + - picard #<3 + - pyslim + - python-newick + - qualimap + - samtools=1.15.1 + - scikit-allel + - seqkit + - slim>=4.0 + - tskit>=0.5.0 + - vcflib=1.0.1 + - vcftools + - pip: + - cyvcf2 + - pixy + - sgkit[vcf] diff --git a/scripts/init-site.sh b/scripts/init_site.sh similarity index 100% rename from scripts/init-site.sh rename to scripts/init_site.sh diff --git a/scripts/post-render.py b/scripts/post_render.py similarity index 57% rename from scripts/post-render.py rename to scripts/post_render.py index 6e7cbd97..740eed65 100755 --- a/scripts/post-render.py +++ b/scripts/post_render.py @@ -1,30 +1,33 @@ #!/usr/bin/env python +"""Perform post rendering tasks""" import errno import logging import os import shutil -def safe_mkdir(dirname): - logging.debug(f"Making directory {dirname}") - if not os.path.exists(dirname): +def safe_mkdir(dname): + """Make directory if it doesn't exist""" + logging.debug("Making directory %s", dname) + if not os.path.exists(dname): try: - os.mkdir(dirname) - except FileNotFoundError as e: - print(e) + os.mkdir(dname) + except FileNotFoundError as exc: + print(exc) raise -def safe_copy(src, dst): - logging.debug(f"Copy {dst} -> {src}") - if not os.path.exists(src): - raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), src) +def safe_copy(source, destination): + """Copy source to destination""" + logging.debug("Copy %s -> %s", destination, source) + if not os.path.exists(source): + raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), source) try: - shutil.copy(src, dst) + shutil.copy(source, destination) except FileExistsError: - logging.debug(f"Path {dst} exists; skipping") - except Exception as e: - print(e) + logging.debug("Path %s exists; skipping", destination) + except Exception as exc: + print(exc) raise diff --git a/scripts/setup-data.py b/scripts/setup_data.py similarity index 77% rename from scripts/setup-data.py rename to scripts/setup_data.py index 48916c69..79cb1ecc 100755 --- a/scripts/setup-data.py +++ b/scripts/setup_data.py @@ -1,4 +1,5 @@ #!/usr/bin/env python +"""Setup data examples for rendering exercises and lectures""" import argparse import errno import logging @@ -7,28 +8,31 @@ import yaml ROOT = os.path.normpath(os.path.join(os.path.dirname(__file__), os.pardir)) - -DATAROOT = os.environ.get("DATA_SOURCE", "pgip_data/data") +DOCROOT = os.path.join(ROOT, "docs") +DATAROOT = os.path.join(DOCROOT, "pgip_data/data") def abspath(path): + """Return absolute path""" return os.path.normpath(os.path.abspath(path)) def safe_link(src, dst, dir_fd): - logging.debug(f"Link {dst} -> {src}") + """Create a symlink from src to dst in directory dir_fd""" + logging.debug("Link %s -> %s", dst, src) if not os.path.exists(src): raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), src) try: os.symlink(src, dst, dir_fd=dir_fd) except FileExistsError: - logging.debug(f"Path {dst} exists; skipping") - except Exception as e: - print(e) + logging.debug("Path %s exists; skipping", dst) + except Exception as exc: + print(exc) raise def main(): + """Setup data examples for rendering exercises and lectures""" parser = argparse.ArgumentParser( prog="setup-data.py", description="Setup data examples for rendering exercises and lectures", @@ -41,15 +45,15 @@ def main(): logging.basicConfig(level=args.loglevel.upper()) - with open(args.config, "r") as fh: + with open(args.config, "r", encoding="utf-8") as fh: pgip_data = yaml.safe_load(fh) # Loop through data and link files for session, dataset in pgip_data.items(): if session.startswith("__"): continue - logging.info(f"Setting up links for {session}") - data = dict() + logging.info("Setting up links for %s", session) + data = {} for x in dataset: if isinstance(x, dict): data.update(**x) diff --git a/scripts/setup-pgip-data.sh b/scripts/setup_pgip_data.sh similarity index 100% rename from scripts/setup-pgip-data.sh rename to scripts/setup_pgip_data.sh