Update python-app.yml

Minimal tasks, just trying to run it.

.github/workflows/python-app.yml

@@ -14,31 +14,35 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
-      - uses: cascode-labs/[email protected]
+      - uses: s-weigand/[email protected]
         with:
-          conda_build_env_filepath: environment.yml
-          # Name of the environemnt to create, if any. This name is used if a name is also indicated in `condaFile`
-          build_options: -c bioconda -c conda-forge
-      - name: lint with flake8
-        run: |
-          conda activate neat
-          # stop the build if there are Python syntax errors or undefined names
-          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-      - name: Execute test_gen_reads
-        run: |
-          conda activate neat
-          cd ${{ github.workspace }}
+          conda-channels: bioconda, conda-forge
+          activate-conda: true
+      - run: |
+          conda env create -f environment.yml -n test_neat
+          conda activate test_neat
           poetry install
-          neat --log-level ERROR --no-log read-simulator -c data/test_config.yml -o test
-      - run: echo "This job's status is ${{ job.status }}."
-      - name: Execute seq_err_model_test
-        run: |
-          cd ${{ github.workspace }}
-          neat --log-level ERROR --no-log model-seq-err -i data/baby.fastq
-      - run: echo "This job's status is ${{ job.status }}." 
+          neat
+      
+#       - name: lint with flake8
+#         run: |
+#           conda activate neat
+#           # stop the build if there are Python syntax errors or undefined names
+#           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+#           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+#           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+#       - name: Execute test_gen_reads
+#         run: |
+#           conda activate neat
+#           cd ${{ github.workspace }}
+#           poetry install
+#           neat --log-level ERROR --no-log read-simulator -c data/test_config.yml -o test
+#       - run: echo "This job's status is ${{ job.status }}."
+#       - name: Execute seq_err_model_test
+#         run: |
+#           cd ${{ github.workspace }}
+#           neat --log-level ERROR --no-log model-seq-err -i data/baby.fastq
+#       - run: echo "This job's status is ${{ job.status }}."