Fixed Imports of Conda Package

README.md

@@ -3,11 +3,12 @@
 Read5 is a python wrapper to read fast5, slow5/blow5 and pod5 files using the same overloaded functions from different APIs.
 
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-teal.svg)](https://www.gnu.org/licenses/gpl-3.0)
-![Python3](https://img.shields.io/badge/Language-Python_3-darkred.svg)
+![PyPI - Python Version](https://img.shields.io/pypi/pyversions/read5)
 
-[![PyPI version](https://badge.fury.io/py/read5.svg)](https://badge.fury.io/py/read5)
+[![PyPI version](https://badge.fury.io/py/read5.svg)](https://badge.fury.io/py/read5) ![PyPI - Downloads](https://img.shields.io/pypi/dm/read5) ![PyPI - Status](https://img.shields.io/pypi/status/read5)
 
-<!-- ![conda](https://img.shields.io/badge/Uses-conda-green.svg) [![Anaconda-Server Badge](https://anaconda.org/jannessp/read5/badges/version.svg)](https://anaconda.org/jannessp/read5) ![Conda](https://img.shields.io/conda/dn/jannessp/read5) [![Conda package](https://anaconda.org/jannessp/read5/badges/latest_release_date.svg)](https://anaconda.org/jannessp/read5) [![Conda package](https://anaconda.org/jannessp/read5/badges/platforms.svg)](https://anaconda.org/jannessp/read5) -->
+
+[![Anaconda-Server Badge](https://anaconda.org/jannessp/read5/badges/version.svg)](https://anaconda.org/jannessp/read5) ![Conda](https://img.shields.io/conda/dn/jannessp/read5) [![Conda package](https://anaconda.org/jannessp/read5/badges/latest_release_date.svg)](https://anaconda.org/jannessp/read5) [![Conda package](https://anaconda.org/jannessp/read5/badges/platforms.svg)](https://anaconda.org/jannessp/read5)
 
 [![DOI](https://zenodo.org/badge/633012569.svg)](https://zenodo.org/badge/latestdoi/633012569)
 
@@ -20,20 +21,26 @@ ___
 ___
 ## Installation
 
-Pod5 is not available via conda (27.06.2023).
-Read5 Currently available via pipy.
-
+### Pypi/pip
 ```bash
 pip install read5
 ```
+### Conda
+Pod5 is currently not available via conda (27.06.2023). Please install it using pip in your conda environment.
+```bash
+conda install mamba
+mamba create -n read5 -c jannessp read5
+conda activate read5
+pip install pod5 # needed as no pod5 conda package available yet
+```
 ___
 ## Usage
 
 [Click here to see a full documentation about the classes and function.](https://jannessp.github.io/read5.github.io/)
 
 *my_file* can be a fast5, slow5, blow5 or pod5 file. The wrapper detects the file format depending on the file extension.
 
-Small example:
+### Small example:
 
 ```python
 from read5 import read # or from read5.Reader import read
@@ -49,6 +56,7 @@ for readid in r5:
 readid_list = r5.getReads()
 ```
 
+### File Reader Classes
 If you want to use the file readers you can import the corresponding class like this:
 
 ```python
@@ -57,6 +65,21 @@ from read5.Slow5Reader import Slow5Reader # contains the Slow5 Reader class
 from read5.Pod5Reader import Pod5Reader # contains the Pod5 Reader class
 ```
 
+### Abstract File Reader Class
+
+```python
+from read5.AbstractFileReader import AbstractFileReader
+```
+
+### Possible Exceptions
+
+```python
+from read5.Exceptions import UnknownFileFormatException, UnknownNormalizationMode
+```
+
+- UnknownFileFormatException: is raised, when the file extension does not match one of ['.fast5', '.slow5', '.blow5', 'pod5']
+- UnknownNormalizationMode: is raised, when an unknown mode is provided for the signal normalization function
+
 ## Full Documentation
 Created with [pdoc3](https://pdoc3.github.io/pdoc/).
 Can be found [here](https://jannessp.github.io/read5.github.io/).

conda.recipe/README.md

@@ -1,5 +1,5 @@
 # Run
 ```bash
-conda mambabuild conda.recipe/ --variants "{python: [3.8, 3.9, 3.10, 3.11]}"
+conda mambabuild conda.recipe/
 conda convert --platform osx-64 /path/to/package.tar.bz2 -o outputdir/
 ```

conda.recipe/conda_build_config.yaml

@@ -0,0 +1,4 @@
+python:
+  - 3.8
+  - 3.9
+  - 3.10

conda.recipe/meta.yaml

@@ -10,29 +10,31 @@ source:
 build:
   # If the installation is complex, or different between Unix and Windows, use
   # separate bld.bat and build.sh files instead of this key.  Add the line
-  skip: true # [py<38]
-  skip: true # [win]
+  # skip: true # [py<38]
+  # skip: true # [win]
   script: {{ PYTHON }} -m pip install --no-deps --ignore-installed -v .
+  # script: python3 setup.py sdist bdist_wheel
 
 requirements:
   host:
-    - python>=3.8
+    - python
     - pip
-    - setuptools
   run:
-    - python>=3.8
-    # dependencies are defined in setup.py
-    {% for dep in data['install_requires'] %}
-    - {{ dep.lower() }}
-    {% endfor %}
+    - python
+    - pyslow5 >=1.0
+    - numpy >=1.20
+    - h5py >=3.8
+    - ont_vbz_hdf_plugin >=1.0
+    # - pod5 >=0.2.3 # currently not available in conda
 
-# TODO: Activate tests when pod5 is available via conda!
+# TODO enable when pod available via conda
 # test:
 #   source_files:
 #     - tests
+#   imports:
+#     - read5
 #   requires:
 #     - pytest
-#     - pytest-cov
 #   commands:
 #     - pytest
 
@@ -42,4 +44,8 @@ about:
   license: {{ data['license'] }}
   license_file: LICENSE
   doc_url: https://github.com/JannesSP/read5.github.io
-  dev_url: {{ data['url'] }}
+  dev_url: {{ data['url'] }}
+
+extra:
+  recipe-maintainers:
+    - JannesSP

pipy.sh

@@ -0,0 +1,3 @@
+python3 -m pip install --user --upgrade setuptools wheel
+python3 setup.py sdist bdist_wheel
+twine upload dist/*

setup.py

@@ -1,14 +1,23 @@
 from setuptools import setup, find_packages
 import versioneer
 
+# conda
+# requirements = [
+#     'python',
+#     'h5py>=3.8',
+#     'ont_vbz_hdf_plugin>=1.0',
+#     'pyslow5>=1.0.0',
+#     'numpy>=1.20',
+# ]
+
+# pipy
 requirements = [
-    # package requirements go here
+    'python>=3.8,<3.11',
     'h5py>=3.0',
-    # 'ont_vbz_hdf_plugin>=1.0',
-    'vbz-h5py-plugin>=1.0', # same as ont_vbz but in pipy
-    'pyslow5>=1.0',
-    'numpy',
-    'pod5>=0.2.3', # currently only avaible via pipy
+    'vbz-h5py-plugin>=1.0',
+    'pyslow5>=1.0.0',
+    'numpy>=1.20',
+    'pod5>=0.2.3',
 ]
 
 with open("README.rst", "r") as rst:
@@ -28,12 +37,14 @@
     install_requires=requirements,
     keywords=['read5', 'slow5', 'blow5', 'fast5', 'pod5', 'ONT', 'Oxford Nanopore Technologies', 'Nanopore', 'raw data', 'wrapper'],
     classifiers=[
+        'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Developers',
+        'Intended Audience :: Science/Research',
         'License :: OSI Approved :: GNU General Public License v3 (GPLv3)',
         'Natural Language :: English',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
-        'Programming Language :: Python :: 3.11',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
     ]
 )