Update gh actions and test

GillesFischerSorbonne · Oct 20, 2023 · 9e209a5 · 9e209a5
1 parent f9ead94
commit 9e209a5
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Showing 5 changed files with 51 additions and 99 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -15,23 +15,32 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: ["3.10"]
+        python: ["3.10", "3.11"]
       fail-fast: false
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.X
-      uses: actions/setup-python@v2
+    - uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: ${{ matrix.python }}
-
-    - name: bedtools
-      run: |
-        sudo apt-get install -y bedtools
+          micromamba-version: '1.3.1-0'
+          cache-environment: true
+          environment-name: installation
+          condarc: |
+              channels:
+                  - conda-forge
+                  - bioconda
+                  - defaults
+          create-args: >-
+            python=${{ matrix.python }}
+            bedtools
+    - name: Checkout repo
+      uses: actions/checkout@v3
+
     - name: Install the package itself
-      run: |
-          pip install .
+      shell: bash -el {0}
+      run: pip install .
+
     - name: Test with pytest
+      shell: bash -el {0}
       run: |
         pip install pytest
         pip install pytest-cov

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,30 @@
+[tool.poetry]
+name = "telofinder"
+version = "1.0.0"
+description = "A python package to determine the location and the size of telomeric repeats (both terminal and internal) from genome assemblies."
+authors = ["Gilles Fischer"]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = ">=3.10,<3.13"
+biopython = "^1.81"
+numpy = "^1.26.1"
+pandas = "^2.1.1"
+pybedtools = "^0.9.1"
+pysam = "^0.22.0"
+python-dateutil = "^2.8.2"
+pytz = "^2023.3.post1"
+six = "^1.16.0"
+numpydoc = "^1.6.0"
+matplotlib = "^3.8.0"
+
+
+[tool.poetry.group.test.dependencies]
+pytest = "^7.4.2"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.scripts]
+telofinder = "telofinder.main:main"
diff --git a/requirements.txt b/requirements.txt
diff --git a/setup.py b/setup.py
diff --git a/test/test_telomer.py b/test/test_telomer.py
@@ -6,4 +6,4 @@
 
 
 def test_run_on_single_fasta():
-    df = tf.run_on_single_fasta(filename, 0.8, 0.8, 8000, 1)
+    df = tf.run_on_single_fasta(filename, 0.8, 0.8, 8000, "both", 1)