From 188e429e094d139bb460f7e60c81b71bbd13cfb3 Mon Sep 17 00:00:00 2001
From: balajtimate <51365402+balajtimate@users.noreply.github.com>
Date: Mon, 16 Oct 2023 21:44:32 +0200
Subject: [PATCH] feat: update dockerfile (#12)

* update conda env

* feat: create separate env for toolz

* update ci

* refactor: update Dockerfile

* update env

* update ci
---
 .../pull_request_template.md                  |  0
 .github/workflows/ci.yml                      | 32 +++++++++----------
 Dockerfile                                    |  7 ++--
 environment-dev.yml                           |  2 +-
 environment.yml                               |  3 +-
 requirements.txt                              |  6 ----
 6 files changed, 21 insertions(+), 29 deletions(-)
 rename pull_request_template.md => .github/pull_request_template.md (100%)

diff --git a/pull_request_template.md b/.github/pull_request_template.md
similarity index 100%
rename from pull_request_template.md
rename to .github/pull_request_template.md
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 4dbe371..90d4a4d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -17,7 +17,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - name: check out repository
+      - name: Check out repository
         uses: actions/checkout@v4
          
       - name: Setup Conda/Mamba
@@ -25,14 +25,14 @@ jobs:
         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/docker-ci-scripts@v5.1.0
         with:
diff --git a/Dockerfile b/Dockerfile
index 682bfbc..2ba76c6 100644
--- 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"]
\ No newline at end of file
+CMD ["transcript-sampler", "-v"]
\ No newline at end of file
diff --git a/environment-dev.yml b/environment-dev.yml
index 0206f25..b1cd936 100644
--- 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
index 576a543..9fde210 100644
--- 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
index 92c62c1..56363d7 100644
--- 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