Update info for pypi, release 0.3.0 (#81)

Author: eburgoswisc

CHANGELOG.md

@@ -1,24 +1,31 @@
 # Changelog
 
-## [0.3.0] - Unreleased
+## [0.3.0] - 2021-07-09
 ### Fixed
-- Refactor demultiplex script
-- Logger is now compatible with snakemake logging
-- Bugs in gbk_convert
+- Refactor demultiplex.py for readability and faster execution
+- Logger is now compatible with snakemake logging module
+- Fixed small parsing bugs in gbk_convert.py
 
 ### Changed
 - Remove third party folder which contained 'bowtie' executables
 - file paths are now handled by pathlib
 - New settings class that is compatible with snakemake
 - The map_reads script is now a stand-alone script
+- Settings class which is used by snakemake and pyinseq
+- Pyinseq and snakemake now use `pathlib` for handling filepaths
+- Removed readthedocs website
+- Removed docs/
+- Removed third-party/
 
 ### Added
-- Workflows are now executed by snakemake
-- Snakefiles for each command of pyinseq
-- New command line parser function
-- Conda environment files to install `bowtie`
-- An option for running pytest on pyinseq
-- New tests for pyinseq
+- Snakemake can now execute workflows using Snakefile in pyinseq
+- Additional Snakefiles for genomprep and demultiplex of pyinseq
+- Conda virtual environment files that allow conda to install `bowtie` software during runtime
+- Parser.py script for parsing command line arguments
+- Include '--test' option for running pytest on pyinseq
+- New pytests for testing workflows in pyinseq
+- Pyinseq will now summarize sample information and snakemake output
+- New user guide for pyinseq
 
 
 ## [0.2.1] - 2021-06-02

LICENSE.md

@@ -1,4 +1,4 @@
-Copyright (c) 2015-2021, Mark J. Mandel  
+Copyright (c) 2015-2021, The Authors  
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or 

MANIFEST.in

@@ -1,2 +1,5 @@
 include pyinseq/VERSION
-graft pyinseq/third-party
+include pyinseq/workflows/PyinseqWorkflow/Snakefile
+include pyinseq/workflows/DemultiplexWorkflow/Snakefile
+include pyinseq/workflows/GenomeprepWorkflow/Snakefile
+include pyinseq/envs/bowtie.yaml

README.md

@@ -127,7 +127,7 @@ $ pyinseq -i <input file> -s <sample file> -g <genbank file> -e <experiment name
 
 - Number of cores to use for execution
 
-`--additional_params`
+`--snakemake_params`
 
 - Additional parameters that will get passed to `snakemake`.
 
@@ -301,7 +301,7 @@ $ pyinseq -i reads.fastq -s samples.txt -g genome.gbk -e pyinseq --threads 4
 
 ```bash
 $ cat demo-run-config.yaml
-additional_params: []
+snakemake_params: []
 barcode_length: 4
 command: pyinseq
 config: false
@@ -322,7 +322,7 @@ transposon_seq: ACAGGTTG
 If you installed **conda** in your terminal, you can use the option `--use-conda` which will install bowtie during the executuion of the workflow. 
 
 ```bash
-$ pyinseq -i reads.fastq -s samples.txt -g genome.gbk -e demo-run --threads 4 --additional_params --use-conda 
+$ pyinseq -i reads.fastq -s samples.txt -g genome.gbk -e demo-run --threads 4 --snakemake_params --use-conda 
 ```
 
 You can also get a default configuration file by using `--get_default_config` and modify it using a text-editor.
@@ -433,7 +433,7 @@ Verify that pyinseq installed correctly by running:
 (pyinseq) $ pyinseq --help
 2021-05-26 13:10 - INFO - pyinseq - Process command line arguments
 usage: pyinseq [-h] [--get_default_config] [--config_format CONFIG_FORMAT]
-               [-c CONFIG] [-t THREADS] [--additional_params ...] [-v]
+               [-c CONFIG] [-t THREADS] [--snakemake_params ...] [-v]
                [-i INPUT] [-s SAMPLES] [-e EXPERIMENT] [-g GENOME]
                [-d DISRUPTION] [--min_count MIN_COUNT] [--max_ratio MAX_RATIO]
                [--barcode_length BARCODE_LENGTH]

RELEASECHECKLIST.md

@@ -1,8 +1,6 @@
 - [ ] Change version number in pyinseq/VERSION
-- [ ] Change short and full version in docs/conf.py
-- [ ] Check copyright date in docs/conf.py
 - [ ] Update CHANGELOG.md, prepare text for GitHub release
 - [ ] Commit changes and ensure that the commit passes tests
 - [ ] Tag the release and push to GitHub
-- [ ] Upload to pypitest: `python setup.py sdist upload -r pypitest`
-- [ ] Upload to pypi: `python setup.py sdist upload -r pypi`
+- [ ] Upload to pypitest: `python3 -m twine upload --repository testpypi dist/*`
+- [ ] Upload to pypi: `python3 -m twine upload dist/*`

pyinseq/VERSION

@@ -1 +1 @@
-0.2.1
+0.3.0

pyinseq/parsers.py

@@ -41,7 +41,7 @@ def get_snake_parser():
         type=int,
     )
     snake_group.add_argument(
-        "--additional_params",
+        "--snakemake_params",
         help="Additional params passed to snakemake. "
         "This should be included at the end of the command since everything will be passed to snakemake so make sure they are correct. "
         "For example, you can use `-n` to check which files snakemake will create without execution the full workflow.",

pyinseq/settings.py

@@ -47,7 +47,7 @@ def __init__(self, config_file):
             "--quiet",
         ]
         # Add additional parameters, if any...
-        self.snakemake_cmd.extend(config_dict["additional_params"])
+        self.snakemake_cmd.extend(config_dict["snakemake_params"])
         self.snakemake_cmd = " ".join(self.snakemake_cmd)
 
     def __repr__(self):

pyinseq/tests/data/input/demultiplex-config.yml

@@ -1,8 +1,7 @@
-additional_params: []
 barcode_length: 4
 command: demultiplex
-config: false
-config_format: yaml
+config: null
+config_format: yml
 disruption: 0.9
 experiment: test_demultiplex
 genome: null
@@ -13,6 +12,7 @@ max_ratio: 10
 min_count: 3
 notrim: false
 samples: ../data/input/example01.txt
+snakemake_params: []
 test: false
 threads: 4
-transposon_seq: ACAGGTTG
+transposon_seq: ACAGGTTG

pyinseq/tests/data/input/genomeprep-config.yml

@@ -1,4 +1,4 @@
-additional_params: []
+snakemake_params: []
 barcode_length: 4
 command: genomeprep
 config: false

pyinseq/tests/data/input/test-pyinseq-config.yml

@@ -1,5 +1,3 @@
-additional_params:
-- --use-conda
 barcode_length: 4
 command: pyinseq
 config: null
@@ -13,6 +11,8 @@ input: ../data/input/example01.fastq
 max_ratio: 10
 min_count: 3
 samples: ../data/input/example01.txt
+snakemake_params:
+- --use-conda
 test: false
 threads: 2
 transposon_seq: ACAGGTTG

pyinseq/tests/test_functions.py

@@ -111,7 +111,7 @@ def test_write_config_file(datadir, tmpdir):
         "0.9",
         "--threads",
         "2",
-        "--additional_params",
+        "--snakemake_params",
         "--use-conda",
     ]
     # Get the Namespace object from argparse

pyinseq/tests/test_script.py

@@ -34,7 +34,7 @@ def test_pyinseq_script(datadir, tmpdir):
         output_name,
         "-d",
         "0.9",
-        "--additional_params",
+        "--snakemake_params",
         "--use-conda",
     ]
     status, out, err = runscript("pyinseq", args, directory=str(tmpdir))
@@ -77,7 +77,7 @@ def test_pyinseq_script_unique_transp_barcode_length(datadir, tmpdir):
         "9",
         "--transposon_seq",
         "TCGCACGG",
-        "--additional_params",
+        "--snakemake_params",
         "--use-conda",
     ]
     status, out, err = runscript("pyinseq", args, directory=str(tmpdir))
@@ -152,7 +152,7 @@ def test_pyinseq_genomeprep_script(datadir, tmpdir):
         output_name,
         "-g",
         gb_fn,
-        "--additional_params",
+        "--snakemake_params",
         "--use-conda",
     ]
     status, out, err = runscript("pyinseq", args, directory=str(tmpdir))
@@ -175,7 +175,7 @@ def test_pyinseq_genomeprep_gff_script(datadir, tmpdir):
         "-g",
         gb_fn,
         "--gff",
-        "--additional_params",
+        "--snakemake_params",
         "--use-conda",
     ]
     status, out, err = runscript("pyinseq", args, directory=str(tmpdir))

setup.cfg

@@ -1,3 +1,62 @@
-[aliases]
-test=pytest
-description-file=README.md
+[metadata]
+name = pyinseq
+version = 0.3.0
+author = 
+    Mark J. Mandel
+    Emanuel Burgos
+    Camille Scott
+    Loren Velasquez
+    Benjamin K. Johnson
+author_email = mandel01@gmail.com
+description = Analysis of transposon insertion sequencing (INSeq) data in Python
+long_description = file: README.md
+long_description_content_type = text/markdown
+license = BSD 3-Clause License
+license_files = LICENSE.md
+url = https://github.com/mjmlab/pyinseq
+project_urls =
+    Documentation = https://github.com/mjmlab/pyinseq/blob/master/README.md
+platforms = MacOS, Linux/Unix
+classifiers =
+    Development Status :: 5 - Production/Stable,
+    Intended Audience :: Science/Research,
+    License :: OSI Approved :: BSD3 License,
+    Operating System :: MacOS :: MacOS X,
+    Operating System :: POSIX,
+    Programming Language :: Python :: 3.6,
+    Programming Language :: Python :: 3.7,
+    Topic :: Scientific/Engineering :: Bio-Informatics,
+
+[options]
+zip_safe = False
+package_dir =
+    = pyinseq
+include_package_data = True
+packages = find:
+package_data =
+    pyinseq/workflows/PyinseqWorkflow/Snakefile
+    workflows/DemultiplexWorkflow/Snakefile
+    workflows/GenomeprepWorkflow/Snakefile
+    envs/bowtie.yaml
+scripts =
+    scripts/pyinseq
+python_requires = >=3.6.*, >=3.7.*
+setup_requires = pytest-runner
+tests_require= pytest
+install_requires =
+    black >=18.9b0
+    matplotlib >=1.5.0
+    seaborn >=0.6.0
+    numpy >=1.10.0
+    pandas >=0.18.1
+    pre-commit >=1.12.0
+    pytest >=2.8.1
+    pytest-cov >=2.4.0
+    codecov >=2.0.5
+    PyYAML >=3.11
+    screed >=0.9
+    snakemake >=5.31.1
+    tqdm >=4.61.2
+
+[options.packages.find]
+where = pyinseq

setup.py

@@ -26,18 +26,15 @@
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
-with open("requirements.txt", "r") as fh:
-    requirements = fh.readlines()
 
 # Collect paths to Snakefile's and ENVS
 snake_data = [
-            "workflows/PyinseqWorkflow/Snakefile",
-            "workflows/DemultiplexWorkflow/Snakefile",
-            "workflows/GenomeprepWorkflow/Snakefile",
-            "envs/bowtie.yaml",
+            "pyinseq/workflows/PyinseqWorkflow/Snakefile",
+            "pyinseq/workflows/DemultiplexWorkflow/Snakefile",
+            "pyinseq/workflows/GenomeprepWorkflow/Snakefile",
+            "pyinseq/envs/bowtie.yaml",
 ]
 
-
 def main():
     setup(
         name="pyinseq",
@@ -46,7 +43,7 @@ def main():
         long_description=long_description,
         long_description_content_type="text/markdown",
         url="https://github.com/mjmlab/pyinseq",
-        author="Mark J. Mandel",
+        author="Mark J. Mandel,Emanuel Burgos,Camille Scott,Loren Velasquez,Benjamin K. Johnson",
         author_email="mandel01@gmail.com",
         license="BSD",
         packages=find_packages(),
@@ -56,18 +53,18 @@ def main():
         scripts=SCRIPTS,
         setup_requires=["pytest-runner"],
         tests_require=["pytest"],
-        install_requires=requirements,
+        python_requires='!=3.8.*,>=3.6.*',
         classifiers=[
             "Development Status :: 4 - Beta",
             "Intended Audience :: Science/Research",
             "License :: OSI Approved :: BSD License",
             "Operating System :: MacOS :: MacOS X",
             "Operating System :: POSIX",
-            "Programming Language :: Python :: 3.5",
+            "Programming Language :: Python :: 3.6",
+            "Programming Language :: Python :: 3.7",
             "Topic :: Scientific/Engineering :: Bio-Informatics",
         ],
         zip_safe=False,
-
     )