Trying to fix metagene installs

XPRESSyourself · Jun 29, 2024 · 3cedb12 · 3cedb12
1 parent a37580a
commit 3cedb12
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Showing 4 changed files with 245 additions and 86 deletions.
diff --git a/.github/workflows/dev-tests.yml b/.github/workflows/dev-tests.yml
@@ -40,20 +40,70 @@ jobs:
         pip install .
         pip install codecov flake8
 
-    - name: Run Tests
+    - name: Run test_arguments.py
       shell: bash -l {0}
       run: |
         conda activate xpresspipe
         coverage run -a tests/test_arguments.py
+
+    - name: Run test_utils.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_utils.py
+
+    - name: Run test_bam.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_bam.py
+
+    - name: Run test_modifyGTF.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_modifyGTF.py
+
+    - name: Run test_truncateGTF.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_truncateGTF.py
+
+    - name: Run test_metagene.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_metagene.py
+
+    - name: Run test_periodicity.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_periodicity.py
+
+    - name: Run test_complexity.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_complexity.py
+
+    - name: Run test_rrnaProbe.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_rrnaProbe.py
+
+    - name: Run test_help.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_help.py
+
+    - name: Run test_pipelines.py
+      shell: bash -l {0}
+      run: |
+        conda activate xpresspipe
         coverage run -a tests/test_pipelines.py
 
     - name: Generate coverage report

diff --git a/.github/workflows/main-tests.yml b/.github/workflows/main-tests.yml
@@ -16,44 +16,93 @@ jobs:
         python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Miniconda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        miniconda-version: "latest"
-        auto-update-conda: true
-        python-version: ${{ matrix.python-version }}
-        activate-environment: xpresspipe
-
-    - name: Install dependencies
-      shell: bash -l {0}
-      run: |
-        conda clean --all
-        conda install -c conda-forge mamba
-        mamba env update --file requirements.yml --name xpresspipe
-        conda activate xpresspipe
-        pip install .
-        pip install codecov flake8
-
-    - name: Run Tests
-      shell: bash -l {0}
-      run: |
-        conda activate xpresspipe
-        coverage run -a tests/test_arguments.py
-        coverage run -a tests/test_utils.py
-        coverage run -a tests/test_bam.py
-        coverage run -a tests/test_modifyGTF.py
-        coverage run -a tests/test_truncateGTF.py
-        coverage run -a tests/test_metagene.py
-        coverage run -a tests/test_periodicity.py
-        coverage run -a tests/test_complexity.py
-        coverage run -a tests/test_rrnaProbe.py
-        coverage run -a tests/test_help.py
-        coverage run -a tests/test_pipelines.py
-
-    - name: Generate coverage report
-      shell: bash -l {0}
-      run: |
-        conda activate xpresspipe
-        coverage report
-        bash <(curl -s https://codecov.io/bash) -cF python
+      - uses: actions/checkout@v3
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: xpresspipe
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          conda clean --all
+          conda env update --file requirements.yml --name xpresspipe
+          conda activate xpresspipe
+          pip install .
+          pip install codecov flake8
+  
+      - name: Run test_arguments.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_arguments.py
+  
+      - name: Run test_utils.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_utils.py
+  
+      - name: Run test_bam.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_bam.py
+  
+      - name: Run test_modifyGTF.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_modifyGTF.py
+  
+      - name: Run test_truncateGTF.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_truncateGTF.py
+  
+      - name: Run test_metagene.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_metagene.py
+  
+      - name: Run test_periodicity.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_periodicity.py
+  
+      - name: Run test_complexity.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_complexity.py
+  
+      - name: Run test_rrnaProbe.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_rrnaProbe.py
+  
+      - name: Run test_help.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_help.py
+  
+      - name: Run test_pipelines.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_pipelines.py
+  
+      - name: Generate coverage report
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage report
+          bash <(curl -s https://codecov.io/bash) -cF python
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -13,43 +13,93 @@ jobs:
         python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Miniconda
-      uses: conda-incubator/setup-miniconda@v2
-      with:
-        miniconda-version: "latest"
-        auto-update-conda: true
-        python-version: ${{ matrix.python-version }}
-        activate-environment: xpresspipe
-
-    - name: Install dependencies
-      shell: bash -l {0}
-      run: |
-        conda clean --all
-        conda env update --file requirements.yml --name xpresspipe
-        conda activate xpresspipe
-        pip install .
-        pip install codecov flake8
-
-    - name: Run Tests
-      shell: bash -l {0}
-      run: |
-        conda activate xpresspipe
-        coverage run -a tests/test_arguments.py
-        coverage run -a tests/test_utils.py
-        coverage run -a tests/test_bam.py
-        coverage run -a tests/test_modifyGTF.py
-        coverage run -a tests/test_truncateGTF.py
-        coverage run -a tests/test_metagene.py
-        coverage run -a tests/test_periodicity.py
-        coverage run -a tests/test_complexity.py
-        coverage run -a tests/test_rrnaProbe.py
-        coverage run -a tests/test_help.py
-        coverage run -a tests/test_pipelines.py
-
-    - name: Generate coverage report
-      shell: bash -l {0}
-      run: |
-        conda activate xpresspipe
-        coverage report
-        bash <(curl -s https://codecov.io/bash) -cF python
+      - uses: actions/checkout@v3
+      - name: Set up Miniconda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          python-version: ${{ matrix.python-version }}
+          activate-environment: xpresspipe
+
+      - name: Install dependencies
+        shell: bash -l {0}
+        run: |
+          conda clean --all
+          conda env update --file requirements.yml --name xpresspipe
+          conda activate xpresspipe
+          pip install .
+          pip install codecov flake8
+  
+      - name: Run test_arguments.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_arguments.py
+  
+      - name: Run test_utils.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_utils.py
+  
+      - name: Run test_bam.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_bam.py
+  
+      - name: Run test_modifyGTF.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_modifyGTF.py
+  
+      - name: Run test_truncateGTF.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_truncateGTF.py
+  
+      - name: Run test_metagene.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_metagene.py
+  
+      - name: Run test_periodicity.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_periodicity.py
+  
+      - name: Run test_complexity.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_complexity.py
+  
+      - name: Run test_rrnaProbe.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_rrnaProbe.py
+  
+      - name: Run test_help.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_help.py
+  
+      - name: Run test_pipelines.py
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage run -a tests/test_pipelines.py
+  
+      - name: Generate coverage report
+        shell: bash -l {0}
+        run: |
+          conda activate xpresspipe
+          coverage report
+          bash <(curl -s https://codecov.io/bash) -cF python
diff --git a/xpresspipe/Rmetagene.r b/xpresspipe/Rmetagene.r
@@ -32,10 +32,20 @@ if (!requireNamespace("dbplyr", quietly = TRUE)) {install.packages("dbplyr", rep
 if (!requireNamespace("data.table", quietly = TRUE)) {install.packages("data.table", repos = "http://cran.us.r-project.org", quiet = TRUE)}
 library(data.table)
 
-if ("GenomicAlignments" %in% rownames(installed.packages()) == FALSE) {
-  BiocManager::install("GenomicAlignments", dependencies=c("Depends", "Imports"), quiet = TRUE)
-} else {
-  print("GenomicAlignments package already installed")
+# Define a function to install a package if not already installed
+install_if_missing <- function(pkg) {
+    if (!pkg %in% rownames(installed.packages())) {
+        BiocManager::install(pkg, dependencies = c("Depends", "Imports"), quiet = FALSE)
+    } else {
+        message(pkg, " package already installed")
+    }
+}
+# List of packages to install
+packages <- c("Rsamtools", "GenomicAlignments")
+
+# Install each package if missing
+for (pkg in packages) {
+    install_if_missing(pkg)
 }
 library(GenomicAlignments)