Ts add test action

.github/workflows/nosetests.yml

@@ -0,0 +1,37 @@
+name: Python package
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9"]
+        os: [ubuntu-latest, macOS-latest]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }} on ${{ matrix.os }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 nose pep8 pyyaml
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # 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: Install
+        run: |
+          python setup.py install
+      - name: Test with nosetests
+        run: |
+          export PYTHONHASHSEED=0
+          nosetests -v tests/test_umi_tools.py

requirements.txt

@@ -8,4 +8,3 @@ regex
 scipy
 matplotlib
 pybktree
-python>=3.5

tests/test_umi_tools.py

@@ -28,8 +28,6 @@
 PYTHON_VERSION = platform.python_version()
 IS_PY3 = sys.version_info.major >= 3
 
-TRAVIS = os.environ.get("TRAVIS", False) == "true"
-JENKINS = os.environ.get("USER", "") == "jenkins"
 
 SUBDIRS = ("gpipe", "optic")
 
@@ -237,7 +235,7 @@ def test_tool():
     fn = 'tests/tests.yaml'
     assert os.path.exists(fn), "tests.yaml does not exist!"
 
-    tool_tests = yaml.load(open(fn))
+    tool_tests = yaml.safe_load(open(fn))
 
     for test, values in sorted(list(tool_tests.items())):
         check_script.description = os.path.join(tool_name, test)
@@ -248,10 +246,6 @@ def test_tool():
                         if PYTHON_VERSION.startswith(x)]
             if len(versions) > 0:
                 continue
-        if "skip_travis" in values and TRAVIS:
-            continue
-        if "skip_jenkins" in values and JENKINS:
-            continue
 
         yield(check_script,
               test,

tests/tests.yaml

@@ -58,7 +58,7 @@ extract_indrop_output_filtered:
       stdin: indrop.fastq.1.gz
       outputs: [stdout, indrop_fuzzy_filtered.1.fastq.gz, indrop_fuzzy_filtered.2.fastq.gz]
       references: [indrop_extract_fuzzy_filtered_out.fastq, indrop_fuzzy_filtered.1.fastq.gz, indrop_fuzzy_filtered.2.fastq.gz]
-      options: umi_tools extract --extract-method=regex --read2-in=<DIR>/indrop.fastq.2.gz --bc-pattern="(?P<cell_1>.{8,12})(?P<discard_2>GAGTGATTGCTTGTGACGCCTT{s<=2})(?P<cell_3>.{8})(?P<umi_1>.{6})T{3}.*" --read2-stdout --error-correct-cell --whitelist=<DIR>/indrop_fuzzy_whitelist.tsv  --filtered-out=indrop_fuzzy_filtered.1.fastq.gz --filtered-out2=indrop_fuzzy_filtered.2.fastq.gz
+      options: extract --extract-method=regex --read2-in=<DIR>/indrop.fastq.2.gz --bc-pattern="(?P<cell_1>.{8,12})(?P<discard_2>GAGTGATTGCTTGTGACGCCTT{s<=2})(?P<cell_3>.{8})(?P<umi_1>.{6})T{3}.*" --read2-stdout --error-correct-cell --whitelist=<DIR>/indrop_fuzzy_whitelist.tsv  --filtered-out=indrop_fuzzy_filtered.1.fastq.gz --filtered-out2=indrop_fuzzy_filtered.2.fastq.gz
 
 extract_scrb_seq_prefiltered:
       stdin: scrb_filtered_fastq.1.gz
@@ -85,7 +85,7 @@ whitelist_indrop:
       stdin: indrop.fastq.1.gz
       outputs: [stdout]
       references: [indrop_whitelist.tsv]
-      options: whitelist --extract-method=regex --bc-pattern="(?P<cell_1>.{8,12})(?P<discard_2>GAGTGATTGCTTGTGACGCCTT)(?P<cell_3>.{8})(?P<umi_1>.{6})T{3}.*" -L test.log 
+      options: whitelist --extract-method=regex --bc-pattern="(?P<cell_1>.{8,12})(?P<discard_2>GAGTGATTGCTTGTGACGCCTT)(?P<cell_3>.{8})(?P<umi_1>.{6})T{3}.*" -L test.log
 
 whitelist_indrop_filtered_out:
       stdin: indrop.fastq.1.gz
@@ -225,7 +225,7 @@ dedup_single_sep:
       stdin: chr19_sep.bam
       outputs: [stdout]
       references: [single_sep_py3.sam]
-      options: "dedup -L test.log --out-sam --random-seed=123456789 --method=directional --umi-separator=:" 
+      options: "dedup -L test.log --out-sam --random-seed=123456789 --method=directional --umi-separator=:"
 
 dedup_single_tag:
       stdin: chr19_tag.bam
@@ -247,10 +247,10 @@ dedup_single_gene_tag:
 
 dedup_paired_umi_whitelist:
       sort: True
-      stdin: whitelist_umi_input.bam 
+      stdin: whitelist_umi_input.bam
       outputs: [stdout]
       references: [whitelist_umi_output.sam]
-      options: dedup --paired --log=test.log --filter-umi --umi-whitelist=<DIR>/umi_whitelist.tsv --umi-whitelist-paired=<DIR>/umi_whitelist.tsv --out-sam --random-seed=123456789 
+      options: dedup --paired --log=test.log --filter-umi --umi-whitelist=<DIR>/umi_whitelist.tsv --umi-whitelist-paired=<DIR>/umi_whitelist.tsv --out-sam --random-seed=123456789
 
 dedup_paired_ignore_tlen_tag:
       stdin: paired.bam
@@ -280,7 +280,7 @@ group_adjacency:
       stdin: chr19.bam
       outputs: [stdout, group_adj_py3.tsv]
       references: [group_adj_py3.sam, group_adj_py3.tsv]
-      options: group -L test.log --out-sam --random-seed=123456789 --method=adjacency --output-bam --out-sam --group-out=group_adj_py3.tsv 
+      options: group -L test.log --out-sam --random-seed=123456789 --method=adjacency --output-bam --out-sam --group-out=group_adj_py3.tsv
 
 group_directional:
       stdin: chr19.bam