feat: update dockerfile (#12)

* update conda env * feat: create separate env for toolz * update ci * refactor: update Dockerfile * update env * update ci
zavolanlab · Oct 16, 2023 · 188e429 · 188e429
1 parent 1992dfa
commit 188e429
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Showing 6 changed files with 21 additions and 29 deletions.
diff --git a/pull_request_template.md → .github/pull_request_template.md b/pull_request_template.md → .github/pull_request_template.md
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -17,22 +17,22 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - name: check out repository
+      - name: Check out repository
         uses: actions/checkout@v4
 
       - name: Setup Conda/Mamba
         uses: conda-incubator/setup-miniconda@v2
         with:
           mamba-version: "*"
           auto-update-conda: true
-          activate-environment: scrnasim
+          activate-environment: scrnasim-toolz
           environment-file: environment.yml
           auto-activate-base: false
 
-      - name: Update scrnasim env with dev packages
-        run: mamba env update -n scrnasim -f environment-dev.yml
+      - name: Update scrnasim-toolz env with dev packages
+        run: mamba env update -n scrnasim-toolz -f environment-dev.yml
 
-      - name: display environment info
+      - name: Display environment info
         run: |
           conda info -a
           conda list
@@ -54,32 +54,32 @@ jobs:
 
     steps:
 
-      - name: checkout repository
+      - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: setup Conda/Mamba
+      - name: Setup Conda/Mamba
         uses: conda-incubator/setup-miniconda@v2
         with:
           mamba-version: "*"
           auto-update-conda: true
-          activate-environment: scrnasim
+          activate-environment: scrnasim-toolz
           environment-file: environment.yml
           auto-activate-base: false
 
-      - name: update scrnasim env with dev packages
-        run: mamba env update -n scrnasim -f environment-dev.yml
+      - name: Update scrnasim-toolz env with dev packages
+        run: mamba env update -n scrnasim-toolz -f environment-dev.yml
 
-      - name: display environment info
+      - name: Display environment info
         run: |
           conda info -a
           conda list
       
-      - name: run unit tests
+      - name: Run unit tests
         run: |
           coverage run --source scRNAsim_toolz -m pytest
           coverage xml
 
-      - name: submit coverage report
+      - name: Submit coverage report
         uses: codecov/codecov-action@v2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -96,14 +96,14 @@ jobs:
 
     steps:
 
-      - name: check out repository
+      - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: generate tag
+      - name: Generate tag
         run: |
           echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV
 
-      - name: build and publish image
+      - name: Build and publish image
         id: docker
         uses: philips-software/[email protected]
         with:

diff --git a/Dockerfile b/Dockerfile
@@ -31,9 +31,8 @@ RUN groupadd -r ${GROUP} && useradd --no-log-init -r -g ${GROUP} ${USER}
 WORKDIR ${WORKDIR}
 RUN chown -R ${USER}:${GROUP} ${WORKDIR} && chmod 700 ${WORKDIR}
 USER ${USER}
-RUN echo "source activate scrnasim" > ~/.bashrc
-ENV PATH /opt/conda/envs/scrnasim/bin:$PATH
+RUN echo "source activate scrnasim-toolz" > ~/.bashrc
+ENV PATH /opt/conda/envs/scrnasim-toolz/bin:$PATH
 
 # SET ENTRYPOINT
-ENTRYPOINT ["transcript-sampler"]
-CMD ["-v"]
+CMD ["transcript-sampler", "-v"]
diff --git a/environment-dev.yml b/environment-dev.yml
@@ -1,4 +1,4 @@
-name: scrnasim
+name: scrnasim-toolz
 channels:
   - conda-forge
   - bioconda

diff --git a/environment.yml b/environment.yml
@@ -1,4 +1,4 @@
-name: scrnasim
+name: scrnasim-toolz
 channels:
   - conda-forge
   - bioconda
@@ -8,7 +8,6 @@ dependencies:
   - polars==0.16.17
   - gtfparse
   - numpy>=1.23.3
-  - nextflow
   - pandas>=1.4.4
   - python>=3.6, <=3.10
   - pyarrow

diff --git a/requirements.txt b/requirements.txt
@@ -1,8 +1,2 @@
-biopython>=1.78
-numpy>=1.23.3
-pandas>=1.4.4
-polars==0.16.17
-gtfparse
 setuptools
-pyarrow
 cli_test_helpers