Merge pull request CCBR#114 from CCBR/pytest

test: setup basic cli tests with pytest

.github/workflows/main.yaml

@@ -12,12 +12,12 @@ jobs:
   Dryrun_Lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: docker://snakemake/snakemake:v5.24.2
       - name: Dry-run pipeline
         run: |
           docker run -v $PWD:/opt2 -w /opt2 snakemake/snakemake:v5.24.2 \
-            python ./renee run \
+            python ./src/renee/__main__.py run \
               --input .tests/KO_S3.R1.fastq.gz .tests/KO_S3.R2.fastq.gz .tests/KO_S4.R1.fastq.gz .tests/KO_S4.R2.fastq.gz .tests/WT_S1.R1.fastq.gz .tests/WT_S1.R2.fastq.gz .tests/WT_S2.R1.fastq.gz .tests/WT_S2.R2.fastq.gz \
               --output output \
               --genome config/genomes/biowulf/hg38_30.json \
@@ -29,3 +29,38 @@ jobs:
         run: |
           docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
           echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'
+
+  Test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: pip
+        run: |
+          python -m pip install --upgrade pip setuptools pytest
+      - name: check CLI basics
+        run: |
+          ./bin/renee --help
+          ./bin/renee --version
+      - name: Test
+        run: |
+          python -m pytest
+
+  build-status: # https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+    runs-on: ubuntu-latest
+    needs: [Dryrun_Lint, Test]
+    if: always()
+    steps:
+      - name: Successful build
+        if: ${{ !(contains(needs.*.result, 'failure')) }}
+        run: exit 0
+      - name: Failing build
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1

bin/redirect

@@ -67,4 +67,4 @@ elif [[ $ISFRCE == true ]];then
 	export PATH="/mnt/projects/CCBR-Pipelines/bin:$PATH"
 fi
 
-${TOOLDIR}/${TOOLNAME} "$@" || true
+${TOOLDIR}/src/renee/__main__.py "$@" || true

renee → src/renee/__main__.py

@@ -25,7 +25,10 @@
 
 # Pipeline Metadata and globals
 # __version__ = "v2.5.2"
-RENEE_PATH = os.path.dirname(os.path.abspath(__file__))
+RENEE_PATH = os.path.dirname(
+    os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+)
+
 vfile = open(os.path.join(RENEE_PATH, "VERSION"), "r")
 __version__ = "v" + vfile.read()
 __version__ = __version__.strip()
@@ -1101,7 +1104,6 @@ def run(sub_args):
         Parsed arguments for run sub-command
     """
     # Get PATH to RENEE git repository for copying over pipeline resources
-    git_repo = os.path.dirname(os.path.abspath(__file__))
 
     # hpcname is either biowulf, frce, or blank
     hpcname = get_hpcname()
@@ -1110,14 +1112,14 @@ def run(sub_args):
     ):
         # Initialize working directory, copy over required pipeline resources
         input_files = initialize(
-            sub_args, repo_path=git_repo, output_path=sub_args.output
+            sub_args, repo_path=RENEE_PATH, output_path=sub_args.output
         )
 
         # Step pipeline for execution, create config.json config file from templates
         config = setup(
             sub_args,
             ifiles=input_files,
-            repo_path=git_repo,
+            repo_path=RENEE_PATH,
             output_path=sub_args.output,
         )
     # load config from existing file
@@ -1370,7 +1372,6 @@ def build(sub_args):
     """
     # Get PATH to RENEE git repository
     # for copying over pipeline resources
-    git_repo = os.path.dirname(os.path.abspath(__file__))
 
     # Build Output directory
     output_path = os.path.abspath(sub_args.output)
@@ -1379,7 +1380,7 @@ def build(sub_args):
     # initialize, copy resources, and
     # generate config file
     additional_bind_paths = configure_build(
-        sub_args=sub_args, git_repo=git_repo, output_path=output_path
+        sub_args=sub_args, git_repo=RENEE_PATH, output_path=output_path
     )
 
     # Add any additional bindpaths
@@ -1588,7 +1589,7 @@ def parsed_arguments(name, description):
 
     # Adding Version information
     parser.add_argument(
-        "--version", action="version", version="%(prog)s {}".format(__version__)
+        "--version", action="version", version="renee {}".format(__version__)
     )
 
     # Create sub-command parser

tests/test_cli.py

@@ -0,0 +1,17 @@
+import pytest
+import subprocess
+from src.renee.__main__ import exists
+
+
+def test_help():
+    output = subprocess.run(
+        "src/renee/__main__.py --help", capture_output=True, shell=True, text=True
+    ).stdout
+    assert "RENEE" in output
+
+
+def test_version():
+    output = subprocess.run(
+        "src/renee/__main__.py --version", capture_output=True, shell=True, text=True
+    ).stdout
+    assert "renee v" in output