fixed autometic version build

.gitignore

@@ -2,6 +2,7 @@
 data/*
 !data/sample_R1.fastq.gz
 !data/sample_R2.fastq.gz
+conda-recipe/record.txt
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

conda-recipe/build.sh

@@ -1,24 +1,8 @@
 #!/bin/sh
 
-mkdir -p $PREFIX/lib/python$PY_VER/site-packages/tests/testdata
-cp -r tests/testdata/* $PREFIX/lib/python$PY_VER/site-packages/tests/testdata/
-
-# Read the "versions" file located one directory up
-VERSION_FILE="../versions"
-
-# Extract the version for "wipertools"
-if [ -f "$VERSION_FILE" ]; then
-    WIPERTOOLS_VERSION=$(grep "^wipertools:" "$VERSION_FILE" | cut -d':' -f2 | tr -d '[:space:]')
-    export WIPERTOOLS_VERSION
-else
-    echo "Error: versions file not found!"
-    exit 1
-fi
-
-WIPERTOOLS_VERSION=1.1.1
-export WIPERTOOLS_VERSION
-
-# # Print the version (optional, for debugging)
-# echo "WIPERTOOLS_VERSION is set to $WIPERTOOLS_VERSION"
+# mkdir -p $PREFIX/lib/python$PY_VER/site-packages/tests/testdata
+# cp -r tests/testdata/* $PREFIX/lib/python$PY_VER/site-packages/tests/testdata/
+mkdir -p $PREFIX/lib/python$PY_VER/site-packages/
+cp versions.json $PREFIX/lib/python$PY_VER/site-packages/
 
 $PYTHON setup.py install --single-version-externally-managed --record=$RECIPE_DIR/record.txt

conda-recipe/meta.yaml

@@ -1,9 +1,5 @@
-{% set data = load_setup_py_data(setup_file="setup.py") %}
-{% set version = data.get('version') %}
-
-# https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html
-# https://docs.conda.io/projects/conda-build/en/latest/resources/define-metadata.html#:~:text=%7B%7B%20version%20%7D%7D-,load_file_data,-%3A%20Parse%20JSON%2C%20TOML
-
+{% set data = load_file_data('versions.json') %}
+{% set version = data.get('wipertools') %}
 {% set sha256 = "898812fc8d2ac86f22f4da9e24eb707383a681c8553aa6813a05b108c8e10582" %}
 
 package:
@@ -23,16 +19,16 @@ build:
   # number: { { environ.get('GITHUB_RUN_NUMBER', 0) } }
   number: 0
   noarch: python
-  # script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
   run_exports:
     - {{ pin_subpackage('wipertools', max_pin="x.x") }}
   entry_points:
     - wipertools = fastqwiper.wipertools:main
+  script_env:
+    - WIPERTOOLS_VERSION={{version}}
 
 requirements:
   host:
     - python >=3.7
-    - pip
     - setuptools
   run:
     - python >=3.7

fastqwiper/summary_gather.py

@@ -15,7 +15,7 @@
 
 class GatherSummaries(WiperTool):
     def __init__(self):
-        super().__init__("summarygatherer")
+        super().__init__("summarygather")
 
     # Inherited methods
     def set_parser(self, parser: argparse.ArgumentParser):
@@ -55,40 +55,67 @@ def parse_summary_file(filepath):
                 if line.startswith(TOTAL_LINES):
                     right = line.split(':')[1]
                     m = re.match(INT_REGEX, right)
-                    data[TOTAL_LINES] = int(m.group('var'))
+                    if(m):
+                        data[TOTAL_LINES] = int(m.group('var'))
+                    else:
+                        raise ValueError(f"TOT_LINES match failed for line: {right}")
                 elif line.startswith(WELLFORMED):
                     right = line.split(':')[1]
                     m = re.match(INT_PERCENT_REGEX, right)
-                    data[WELLFORMED] = int(m.group('var'))
+                    if m:
+                        raise ValueError(f"WELLFORMED match failed for line: {right}")
+                    else:
+                        data[WELLFORMED] = 0
                 elif line.startswith(CLEAN):
                     right = line.split(':')[1]
                     m = re.match(INT_REGEX, right)
-                    data[CLEAN] = int(m.group('var'))
+                    if m:
+                        data[CLEAN] = int(m.group('var'))
+                    else:
+                        raise ValueError(f"CLEAN match failed for line: {right}")
                 elif line.startswith(MISPLACED_HEADER):
                     right = line.split(':')[1]
                     m = re.match(INT_INT_REGEX, right)
-                    data[MISPLACED_HEADER] = int(m.group('var'))
-                    data[RECOVERED_HEADER] = int(m.group('var2'))
+                    if m:
+                        data[MISPLACED_HEADER] = int(m.group('var'))
+                        data[RECOVERED_HEADER] = int(m.group('var2'))
+                    else:
+                        raise ValueError(f"MISPLACED_HEADER and RECOVERED_HEADER match failed for line: {right}")
                 elif line.startswith(BAD_SEQ):
                     right = line.split(':')[1]
                     m = re.match(INT_PERCENT_REGEX, right)
-                    data[BAD_SEQ] = int(m.group('var'))
+                    if m:
+                        data[BAD_SEQ] = int(m.group('var'))
+                    else:
+                        raise ValueError(f"BAD_SEQ match failed for line: {right}")
                 elif line.startswith(BAD_PLUS):
                     right = line.split(':')[1]
                     m = re.match(INT_PERCENT_REGEX, right)
-                    data[BAD_PLUS] = int(m.group('var'))
+                    if m:
+                        data[BAD_PLUS] = int(m.group('var'))
+                    else:
+                        raise ValueError(f"BAD_PLUS match failed for line: {right}")
                 elif line.startswith(BAD_QUAL):
                     right = line.split(':')[1]
                     m = re.match(INT_PERCENT_REGEX, right)
-                    data[BAD_QUAL] = int(m.group('var'))
+                    if m:
+                        data[BAD_QUAL] = int(m.group('var'))
+                    else:
+                        raise ValueError(f"BAD_QUAL match failed for line: {right}")
                 elif line.startswith(LENGTH_SEQ_QUAL):
                     right = line.split(':')[1]
                     m = re.match(INT_REGEX, right)
-                    data[LENGTH_SEQ_QUAL] = int(m.group('var'))
+                    if m:
+                        data[LENGTH_SEQ_QUAL] = int(m.group('var'))
+                    else:
+                        raise ValueError(f"LENGTH_SEQ_QUAL match failed for line: {right}")
                 elif line.startswith(BLANKS):
                     right = line.split(':')[1]
                     m = re.match(INT_PERCENT_REGEX, right)
-                    data[BLANKS] = int(m.group('var'))
+                    if m:
+                        data[BLANKS] = int(m.group('var'))
+                    else:
+                        raise ValueError(f"BLANKS match failed for line: {right}")
 
             return data
 

fastqwiper/wipertool_abstract.py

@@ -1,5 +1,6 @@
 from abc import ABC, abstractmethod
 from argparse import Namespace
+import json
 import os
 
 
@@ -10,9 +11,9 @@ class WiperTool(ABC):
     def __init__(self, name):
         self.name = name
 
-        versions_file_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'versions')
-        with open(versions_file_path, 'r') as file:
-            self.config = {line.split(':')[0]: line.split(':')[1].strip() for line in file if line.strip()}
+        versions_file_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'versions.json')
+        with open(versions_file_path) as f:
+            self.config = json.load(f)
 
     def version(self):
         return self.config.get(self.name, "")

fastqwiper/wipertools.py

@@ -1,4 +1,5 @@
 import sys
+import json
 import os.path
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
@@ -12,6 +13,8 @@
 
 def main():
     parser = argparse.ArgumentParser(description='FastqWiper program help')
+    parser.add_argument('-v', '--version', action='version', version=version(), help='It prints the version and exists')
+
     subparsers = parser.add_subparsers(help='Choices', dest='selected_subparser')
 
     # create the parser for the FastqWiper main program
@@ -30,7 +33,7 @@ def main():
     fg.set_parser(fg_parser)
 
     # create the parser for the gather_summaries program
-    sg_parser = subparsers.add_parser('summarygather', help='Gatherer of FastqWiper summary files')
+    sg_parser = subparsers.add_parser('summarygather', help='Summary gather program')
     sg = GatherSummaries()
     sg.set_parser(sg_parser)
 
@@ -49,5 +52,11 @@ def main():
         parser.print_help()
 
 
+def version():
+    versions_file_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'versions.json')
+    with open(versions_file_path) as f:
+        config = json.load(f)
+        return config.get("wipertools", "")
+
 if __name__ == "__main__":
     main()

setup.py

@@ -1,24 +1,17 @@
 import os
 from setuptools import setup, find_packages
 
-# version='0.0.1'
-# if '--wipertools_version' in sys.argv:
-#      version_idx = sys.argv.index('--wipertools_version')
-#      version = sys.argv[version_idx + 1]
-#      sys.argv.remove('--wipertools_version')
-#      sys.argv.pop(version_idx)
-
 version_string = os.environ.get("WIPERTOOLS_VERSION", "0.0.0.dev0")
 
 setup(
     name="wipertools",
     version=version_string,
-    packages=find_packages(),
+    packages=find_packages(exclude=("tests",)),
     # https://setuptools.pypa.io/en/latest/userguide/datafiles.html
     # package_data={"": ["*.txt"], "mypkg1": ["data1.rst"]},
     # include_package_data=True,
-    # exclude_package_data={"mypkg": [".gitattributes"]},
-    install_requires=["setuptools"],
+    # exclude_package_data={"tests": [""]},
+    install_requires=[],
     entry_points={
         "console_scripts": [
             "wipertools=fastqwiper.wipertools:main"

versions.json

@@ -0,0 +1,7 @@
+{
+    "wipertools": "1.1.0",
+    "fastqwiper": "1.0.1",
+    "fastqscatter": "1.0.0",
+    "fastqgather": "1.0.0",
+    "summarygather": "1.0.0"
+}