version handling unstable

.devcontainer/devcontainer.json

@@ -20,5 +20,7 @@
         "ms-azuretools.vscode-docker"
       ]
     }
-  }
+  },
+  // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+  "remoteUser": "root"
 }

conda-recipe/build.sh

@@ -1,3 +1,24 @@
 #!/bin/sh
-# $PYTHON setup.py install --single-version-externally-managed --record=$RECIPE_DIR/record.txt
-$PYTHON -m pip install --no-deps --ignore-installed .
+
+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 $WIPERTOOLS_VERSION"
+
+$PYTHON setup.py install --single-version-externally-managed --record=$RECIPE_DIR/record.txt

conda-recipe/meta.yaml

@@ -1,31 +1,41 @@
+{% 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 sha256 = "898812fc8d2ac86f22f4da9e24eb707383a681c8553aa6813a05b108c8e10582" %}
+
 package:
   name: wipertools
-  version: {{ wipertools_version }}
+  version: {{ version }}
 
 #app:
 #  icon: icon_64x64.png
 
 source:
   # git_url: https://github.com/mazzalab/fastqwiper.git
-  path: ./
+  path: ../
+  # url: https://github.com/mazzalab/fastqwiper/archive/refs/tags/2024_11.zip
+  # sha256: {{ sha256 }}
 
 build:
   # number: { { environ.get('GITHUB_RUN_NUMBER', 0) } }
   number: 0
   noarch: python
-  # script: python -m pip install --no-deps --ignore-installed .
+  # 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
 
 requirements:
   host:
-    - python
+    - python >=3.7
     - pip
-
+    - setuptools
   run:
-    - python
+    - python >=3.7
 
 test:
   imports:
@@ -43,3 +53,4 @@ about:
 extra:
   recipe-maintainers:
     - mazzalab
+    - irongraft

conda-recipe/record.txt

@@ -0,0 +1,25 @@
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/tests/test_fastq_wiper.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/tests/__init__.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/wipertools.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/fastq_gather.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/summary_gather.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/fastq_wiper.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/__init__.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/fastq_scatter.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/wipertool_abstract.py
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/tests/__pycache__/test_fastq_wiper.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/tests/__pycache__/__init__.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/__pycache__/wipertools.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/__pycache__/fastq_gather.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/__pycache__/summary_gather.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/__pycache__/fastq_wiper.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/__pycache__/__init__.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/__pycache__/fastq_scatter.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/fastqwiper/__pycache__/wipertool_abstract.cpython-313.pyc
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/wipertools-1.1.1-py3.13.egg-info/SOURCES.txt
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/wipertools-1.1.1-py3.13.egg-info/dependency_links.txt
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/wipertools-1.1.1-py3.13.egg-info/PKG-INFO
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/wipertools-1.1.1-py3.13.egg-info/entry_points.txt
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/wipertools-1.1.1-py3.13.egg-info/top_level.txt
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/python3.13/site-packages/wipertools-1.1.1-py3.13.egg-info/requires.txt
+/opt/conda/conda-bld/wipertools_1731963283217/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/bin/wipertools

fastqwiper/wipertool_abstract.py

@@ -1,23 +1,21 @@
 from abc import ABC, abstractmethod
 from argparse import Namespace
 import os
-import yaml
 
 
 class WiperTool(ABC):
     name: str
-    config: str
+    config: dict
 
     def __init__(self, name):
         self.name = name
-
-        yaml_file_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'conda-recipe', 'conda_build_config.yaml')
-        # Read the YAML file
-        with open(yaml_file_path, 'r') as yaml_file:
-            self.config = yaml.safe_load(yaml_file)
+
+        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()}
 
     def version(self):
-        return self.config.get(self.name + "_version", [None])[0]
+        return self.config.get(self.name, "")
 
     @abstractmethod
     def set_parser(self, parser):

setup.py

@@ -0,0 +1,39 @@
+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(),
+    # 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"],
+    entry_points={
+        "console_scripts": [
+            "wipertools=fastqwiper.wipertools:main"
+        ]
+    },
+    author="Tommaso Mazza",
+    author_email="[email protected]",
+    description="A suite of programs that drop or fix pesky lines in FASTQ files and that split or merge FASTQ chunk files.",
+    long_description=open("README.md").read() if os.path.exists("README.md") else "",
+    long_description_content_type="text/markdown",
+    url="https://github.com/mazzalab/fastqwiper",
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License",
+        "Operating System :: OS Independent",
+    ],
+    python_requires='>=3.7',
+)

versions

@@ -0,0 +1,5 @@
+wipertools:1.1.0
+fastqwiper:1.0.1
+fastqscatter:1.0.0
+fastqgather:1.0.0
+summarygather:1.0.0