Merge pull request #11 from cribbslab/AC-py13

updated github actions so py3.10+ tested

.github/workflows/python-package.yml

@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.7", "3.8"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     defaults:
       run:
@@ -35,20 +35,26 @@ jobs:
           key:
             ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
             hashFiles('conda/environment.yml') }}
+      - name: Set installer URL
+        id: set-installer-url
+        run: |
+          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
+            echo "installer-url=https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh" >> $GITHUB_ENV
+          fi
       - uses: conda-incubator/setup-miniconda@v2
         with:
+          installer-url: ${{ env.installer-url }}
           python-version: ${{ matrix.python-version }}
           channels: conda-forge, bioconda, defaults
           channel-priority: true
           activate-environment: tallytrin
           environment-file: conda/environment.yml
-          miniforge-variant: Mambaforge
       - name: Show conda
         run: |
           conda info
           conda list
           mamba list
-        
+
       - name: Install tallytrin
         run: pip install -e .
       - name: Lint with flake8

tallytrin/entry.py

@@ -12,7 +12,7 @@
 
     tallytrin --help
 
-To get help for a specify workflow, type::
+To get help for a specific workflow, type::
 
     tallytrin <workflow> --help
 '''
@@ -21,20 +21,20 @@
 import sys
 import re
 import glob
-import imp
+import importlib.util
 import tallytrin
 
 
-def printListInColumns(l, ncolumns):
-    '''output list *l* in *ncolumns*.'''
+def print_list_in_columns(l, ncolumns):
+    '''Output list *l* in *ncolumns*.'''
     ll = len(l)
 
     if ll == 0:
         return
 
     max_width = max([len(x) for x in l]) + 3
     n = ll // ncolumns
-    if ll % 3 != 0:
+    if ll % ncolumns != 0:
         n += 1
 
     # build columns
@@ -60,7 +60,6 @@ def main(argv=None):
     argv = sys.argv
 
     # paths to look for pipelines:
-    #print(pipelines.__file__)
     path = os.path.abspath(os.path.dirname(tallytrin.__file__))
     relpath = os.path.abspath("../src")
 
@@ -73,7 +72,7 @@ def main(argv=None):
         print((globals()["__doc__"]))
         print("The list of available pipelines are:\n")
         print("{}\n".format(
-            printListInColumns(
+            print_list_in_columns(
                 sorted([os.path.basename(x)[len("pipeline_"):-len(".py")] for x in pipelines]),
                 2)))
         return
@@ -85,9 +84,21 @@ def main(argv=None):
     # remove 'tallytrin' from sys.argv
     del sys.argv[0]
 
-    (file, pathname, description) = imp.find_module(pipeline, paths)
-
-    module = imp.load_module(pipeline, file, pathname, description)
+    spec = None
+    for path in paths:
+        try:
+            spec = importlib.util.spec_from_file_location(pipeline, os.path.join(path, f"{pipeline}.py"))
+            if spec is not None:
+                break
+        except FileNotFoundError:
+            continue
+
+    if spec is None or spec.loader is None:
+        print(f"Error: pipeline '{command}' not found.")
+        sys.exit(1)
+
+    module = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(module)
 
     module.main(sys.argv)
 

tests/test_style.py

@@ -1,78 +1,50 @@
-'''test_style
-=============
-
-Purpose
--------
-
-Runs pep8 style tests - could be removed if you dont want to
-conform to pep8 for this project?
-
-This script is best run within nosetests::
-
-   nosetests tests/test_style.py
-
-'''
-import pep8
+import pycodestyle
 import glob
 import os
-from nose.tools import ok_
 
 # DIRECTORIES to examine
 EXPRESSIONS = (
     ('FirstLevel', 'scpipelines/*.py'),
     ('SecondLevel', 'scpipelines/version.py'))
 
-# Codes to ignore in the pep8 BaseReport
-IGNORE = set(('E101',  # indentation contains mixed spaces and tabs
-              'E201',  # whitespace after '('
-              'E202',  # whitespace before ')'
-              'E122',  # continuation line missing indentation or outdented
-              'E265',  # block comment should start with '# '
-              'E501',  # line too long (82 > 79 characters)
-              'E502',  # the backslash is redundant between brackets
-              'E731',  # do not assign a lambda expression, use a def
-              'W191',
-              'W291',
-              'W293',
-              'W391',
-              'W503',  # line break before binary operator
-              'W601',
-              'W602',
-              'files',
-              'directories',
-              'physical lines',
-              'logical lines',))
+# Codes to ignore in the pycodestyle BaseReport
+IGNORE = {
+    'E101',  # indentation contains mixed spaces and tabs
+    'E201',  # whitespace after '('
+    'E202',  # whitespace before ')'
+    'E122',  # continuation line missing indentation or outdented
+    'E265',  # block comment should start with '# '
+    'E501',  # line too long (82 > 79 characters)
+    'E502',  # the backslash is redundant between brackets
+    'E731',  # do not assign a lambda expression, use a def
+    'W191',
+    'W291',
+    'W293',
+    'W391',
+    'W503',  # line break before binary operator
+    'W601',
+    'W602'
+}
 
 
 def check_style(filename):
-    '''check style of filename.
-    '''
+    '''check style of filename.'''
 
-    p = pep8.StyleGuide(quiet=True)
-    report = p.check_files([filename])
+    style_guide = pycodestyle.StyleGuide(quiet=True, ignore=IGNORE)
+    report = style_guide.check_files([filename])
 
-    # count errors/warning excluding
-    # those to ignore
-    take = [y for x, y
-            in list(report.counters.items()) if x not in IGNORE]
-    found = ['%s:%i' % (x, y) for x, y
-             in list(report.counters.items()) if x not in IGNORE]
-    total = sum(take)
-    ok_(total == 0,
-        'pep8 style violations: %s' % ','.join(found))
+    # count errors/warnings excluding those to ignore
+    assert report.total_errors == 0, f"Style violations in {filename}"
 
 
 def test_style():
-    '''test style of scripts
-    '''
+    '''test style of scripts'''
 
     for label, expression in EXPRESSIONS:
-
         files = glob.glob(expression)
         files.sort()
 
         for f in files:
             if os.path.isdir(f):
                 continue
-            check_style.description = os.path.abspath(f)
-            yield(check_style, os.path.abspath(f))
+            yield check_style, os.path.abspath(f)