Refactor interface (#88)

* Update setup.cfg for new structure

* Update name

* Update tests for new structure

* Setup pipeval main module

* Update validate module

* Update validate module with new structure

* Update checksum module

* Remove old structure

* Update Dockerfile

* Update command name

* Update CHANGELOG

* Update commands in README

* Remove version from subcommands

CHANGELOG.md

@@ -11,6 +11,18 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
+## [5.0.0-rc.1] - 2023-11-22
+### Changed
+- Restructured CLI to have common main command `pipeval`
+
+---
+
+## [4.0.0] - 2023-11-22
+### Added
+- Parallelize validation
+
+---
+
 ## [4.0.0-rc.2] - 2023-04-24
 ### Changed
 - Resolve potential symlinks before validation

README.md

@@ -70,16 +70,15 @@ pip install .
 ```
 
 ## Usage
-### `validate`
+### `pipeval validate`
 ```
-usage: validate [-h] [-v] [-r CRAM_REFERENCE] path [path ...]
+usage: pipeval validate [-h] [-v] [-r CRAM_REFERENCE] path [path ...]
 
 positional arguments:
   path                  one or more paths of files to validate
 
 options:
   -h, --help            show this help message and exit
-  -v, --version         show program's version number and exit
   -r CRAM_REFERENCE, --cram-reference CRAM_REFERENCE
                         Path to reference file for CRAM
   -p PROCESSES, --processes PROCESSES
@@ -111,9 +110,9 @@ Input: path/to/input is valid <file-type>
 Error: path/to/input <error message>
 ```
 
-### `generate-checksum`
+### `pipeval generate-checksum`
 ```
-usage: generate-checksum [-h] [-t {md5,sha512}] [-v] path [path ...]
+usage: pipeval generate-checksum [-h] [-t {md5,sha512}] [-v] path [path ...]
 
 positional arguments:
   path                  one or more paths of files to validate
@@ -122,7 +121,6 @@ options:
   -h, --help            show this help message and exit
   -t {md5,sha512}, --type {md5,sha512}
                         Checksum type
-  -v, --version         show program's version number and exit
 ```
 
 ## Development

docker/Dockerfile

@@ -32,8 +32,7 @@ RUN mkdir -p /tool/validate/
 COPY setup.py /tool
 COPY setup.cfg /tool
 COPY pyproject.toml /tool
-COPY /generate_checksum /tool/generate_checksum
-COPY /validate/ /tool/validate/
+COPY /pipeval /tool/pipeval
 WORKDIR /tool
 RUN pip install build && \
     pip install .
@@ -48,5 +47,5 @@ RUN groupadd -g 500001 bldocker && \
 # Change the default user to bldocker from root
 USER bldocker
 
-LABEL   maintainer="Arpi Beshlikyan <abeshlikyan@mednet.ucla.edu>" \
-        org.opencontainers.image.source=https://github.com/uclahs-cds/public-tool-PipeVal
+LABEL   maintainer="Yash Patel <yashpatel@mednet.ucla.edu>" \
+        org.opencontainers.image.source=https://github.com/uclahs-cds/package-PipeVal

pipeval/__init__.py

@@ -0,0 +1,3 @@
+'''Inits pipeval module'''
+
+__version__ = '5.0.0-rc.1'

pipeval/__main__.py

@@ -0,0 +1,32 @@
+''' Console script main entrance '''
+import argparse
+from pipeval import __version__
+
+from pipeval.validate.__main__ import add_subparser_validate
+from pipeval.generate_checksum.__main__ import add_subparser_generate_checksum
+
+def _parse_args():
+    """ Parse arguments """
+    parser = argparse.ArgumentParser(
+        prog = 'pipeval'
+    )
+
+    parser.add_argument(
+        '-v', '--version',
+        action='version',
+        version=f'%(prog)s {__version__}'
+    )
+
+    subparsers = parser.add_subparsers(dest = 'command')
+    add_subparser_validate(subparsers)
+    add_subparser_generate_checksum(subparsers)
+
+    return parser.parse_args()
+
+def main():
+    ''' Main entrance '''
+    args = _parse_args()
+    args.func(args)
+
+if __name__=='__main__':
+    main()

generate_checksum/__init__.py → pipeval/generate_checksum/__init__.py

@@ -1,3 +1 @@
 '''Inits checksum module'''
-
-__version__ = '3.0.0'

pipeval/generate_checksum/__main__.py

@@ -0,0 +1,18 @@
+''' Console script main entrance '''
+import argparse
+from pipeval.generate_checksum.checksum import generate_checksum
+
+def add_subparser_generate_checksum(subparsers:argparse._SubParsersAction):
+    """ Parse arguments """
+    parser = subparsers.add_parser(
+        name = 'generate-checksum',
+        help = 'Generate checksums for one or more file(s)',
+        description = 'Generate checksums for one or more file(s)',
+        formatter_class = argparse.ArgumentDefaultsHelpFormatter
+    )
+    parser.add_argument('path', help='one or more paths of files to validate', type=str, nargs='+')
+    parser.add_argument('-t', '--type', help='Checksum type',
+        choices=['md5', 'sha512'],
+        default='sha512')
+
+    parser.set_defaults(func=generate_checksum)

validate/__init__.py → pipeval/validate/__init__.py

@@ -1,3 +1 @@
 '''Inits validate module'''
-
-__version__ = '4.0.0'

validate/__main__.py → pipeval/validate/__main__.py

@@ -1,7 +1,6 @@
 ''' Console script main entrance '''
 import argparse
-from validate import __version__
-from validate.validate import run_validate
+from pipeval.validate.validate import run_validate
 
 def positive_integer(arg):
     """ Type and value check for positive integers """
@@ -15,24 +14,19 @@ def positive_integer(arg):
 
     return i
 
-def _parse_args():
+def add_subparser_validate(subparsers:argparse._SubParsersAction):
     """ Parse arguments """
-    parser = argparse.ArgumentParser()
-    parser.add_argument('path', help='one or more paths of files to validate', type=str, nargs='+')
-    parser.add_argument('-v', '--version', action='version', version=f'%(prog)s {__version__}')
+    parser = subparsers.add_parser(
+        name = 'validate',
+        help = 'Validate one or more file(s)',
+        description = 'Validate one or more file(s)',
+        formatter_class = argparse.ArgumentDefaultsHelpFormatter
+    )
+
+    parser.add_argument('path', help='One or more paths of files to validate', type=str, nargs='+')
     parser.add_argument('-r', '--cram-reference', default=None, \
         help='Path to reference file for CRAM')
     parser.add_argument('-p', '--processes', type=positive_integer, default=1, \
         help='Number of processes to run in parallel when validating multiple files')
 
     parser.set_defaults(func=run_validate)
-
-    return parser.parse_args()
-
-def main():
-    ''' Main entrance '''
-    args = _parse_args()
-    args.func(args)
-
-if __name__=='__main__':
-    main()

validate/validate.py → pipeval/validate/validate.py

@@ -6,16 +6,16 @@
 import multiprocessing
 from itertools import repeat
 
-from validate.validators.bam import _check_bam
-from validate.validators.sam import _check_sam
-from validate.validators.cram import _check_cram
-from validate.validators.vcf import _check_vcf
-from validate.files import (
+from pipeval.validate.validators.bam import _check_bam
+from pipeval.validate.validators.sam import _check_sam
+from pipeval.validate.validators.cram import _check_cram
+from pipeval.validate.validators.vcf import _check_vcf
+from pipeval.validate.files import (
     _check_compressed,
     _path_exists
 )
-from validate.validate_types import ValidateArgs
-from generate_checksum.checksum import _validate_checksums
+from pipeval.validate.validate_types import ValidateArgs
+from pipeval.generate_checksum.checksum import _validate_checksums
 
 # Currently supported data types
 FILE_TYPES_DICT = {

validate/validators/bam.py → pipeval/validate/validators/bam.py

@@ -4,7 +4,7 @@
 
 import pysam
 
-from validate.validate_types import ValidateArgs
+from pipeval.validate.validate_types import ValidateArgs
 
 def _validate_bam_file(path:Path):
     '''Validates bam file'''

validate/validators/cram.py → pipeval/validate/validators/cram.py

@@ -4,7 +4,7 @@
 
 import pysam
 
-from validate.validate_types import ValidateArgs
+from pipeval.validate.validate_types import ValidateArgs
 
 def _validate_cram_file(path:Path, reference:str=None):
     '''Validates cram file'''

validate/validators/sam.py → pipeval/validate/validators/sam.py

@@ -4,7 +4,7 @@
 
 import pysam
 
-from validate.validate_types import ValidateArgs
+from pipeval.validate.validate_types import ValidateArgs
 
 def _validate_sam_file(path:Path):
     '''Validates sam file'''

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
-name = validate
-version = attr: validate.__version__
+name = pipeval
+version = attr: pipeval.__version__
 author = 'Yash Patel'
 author_email = 'YashPatel@mednet.ucla.edu'
 description = 'Python CLI tool to validate different file types and their contents in Nextflow scripts/pipelines'
@@ -31,5 +31,4 @@ where = .
 
 [options.entry_points]
 console_scripts =
-    validate = validate.__main__:main
-    generate-checksum = generate_checksum.__main__:main
+    pipeval = pipeval.__main__:main