Add checks

.bumpversion.cfg

@@ -0,0 +1,19 @@
+[bumpversion]
+commit = True
+tag = True
+current_version = 1.0.0-dev
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}
+	{major}.{minor}.{patch}
+
+[bumpversion:file:setup.py]
+
+[bumpversion:file:./src/pycompressor/__init__.py]
+
+[bumpversion:part:release]
+optional_value = prod
+first_value = dev
+values = 
+	dev
+	prod

.github/workflows/deploy_doc.yml

@@ -20,9 +20,9 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install packages 📦
         run: |
-          # install pip
           python -m pip install --upgrade pip
-          pip install .[docs]
+          pip install .
+          pip install -r docs-requirements.txt
       - name: Build 🔨
         run: |
           cd doc/

.github/workflows/pytest.yml

@@ -47,7 +47,7 @@ jobs:
     - name: Test modules and coverage with pytest
       shell: bash --login {0}
       run: |
-        pip install .[tests]
+        pip install -r tests-requirements.txt
         pytest -v tests/ --cov=./src/pycompressor --cov-report=xml
     - name: Upload coverage report
       uses: codecov/codecov-action@v1

docs-requirements.txt

@@ -0,0 +1,3 @@
+recommonmark
+sphinx_rtd_theme
+sphinxcontrib-bibtex

ganpdfs.yml

@@ -70,3 +70,4 @@ nd_steps   : 4                                       # Number of steps to train
 ng_steps   : 3                                       # Number of steps to train the Generator for one training run
 batch_size : 70                                      # Batch size per epoch in terms of percentage
 epochs     : 1000                                    # Number of epochs
+pdf: NNPDF40_nnlo_as_0118_1000

requirements.txt

@@ -0,0 +1,6 @@
+cma
+numpy
+numba
+rich
+scipy
+tqdm

runcard.yml

@@ -2,7 +2,7 @@
 # PDF Set                                         #
 ###################################################
 pdfsetting:
-  pdf: NNPDF40_nnlo_as_0118_1000rep
+  pdf: NNPDF40_nnlo_as_0118_1000
   existing_enhanced: False
 
 ###################################################

setup.py

@@ -1,102 +1,54 @@
 """
-pyCompressor is a Python implementation of a compressor code
-presented in this paper https://arxiv.org/pdf/1504.06469 and
-implemented here https://github.com/scarrazza/compressor.
+pyCompressor is q python package for Monte Carlo Parton Distribution Functions
+(PDFs) compression.
 
-This program has been developed within the N3PDF group.
-(n3pdf.mi.infn.it/)
+This program has been developed within the N3PDF group. (n3pdf.mi.infn.it/)
 
 Authors: - Stefano Carrazza
-         - Juan Cruz-Martinez
+         - Juan M. Cruz-Martinez
          - Tanjona R. Rabemananjara
 
 License: GPL-3.0, 2020
 """
 
 
-import os
-import re
+import pathlib
 from setuptools import setup
 from setuptools import find_packages
 
 PACKAGE = "pycompressor"
+THIS_DIR = pathlib.Path(__file__).parent
+LONG_DESCRIPTION = (THIS_DIR / "README.md").read_text()
+REQUIREMENTS = (THIS_DIR / "requirements.txt").read_text()
 
-# Used for pytest and code coverage
-TESTS_REQUIEREMENTS = [
-        "pylint",
-        "pytest",
-        "pytest-cov",
-        "pytest-env",
-        "pygit2",
-        "semver"
-    ]
-
-# Dependencies for the packages
-PACKAGE_REQUIEREMENTS = [
-        "cma",
-        "tqdm",
-        "scipy",
-        "numpy",
-        "numba",
-        "rich"
-    ]
-
-# Depending on the documents more dependencies can be added
-DOCS_REQUIEREMENTS = [
-        "recommonmark",
-        "sphinx_rtd_theme",
-        "sphinxcontrib-bibtex"
-    ]
-
-# Check if LHAPDF is installed
 try:
     import lhapdf
 except ImportError:
     print(f"Note: {PACKAGE} requires the installation of LHAPDF")
 
-# Check if Validphys is installed
 try:
     import validphys
 except ImportError:
     print(f"Note: {PACKAGE} requires the installation of VALIDPHYS")
 
-# Read through Readme
-try:
-    this_directory = os.path.abspath(os.path.dirname(__file__))
-    with open(os.path.join(this_directory, "README.md"), encoding="utf-8") as f:
-        long_description = f.read()
-except IOError:
-    print("Read me file not found.")
-
-
-# Get package version
-def get_version():
-    """
-    Gets the version from the package's __init__ file
-    if there is some problem, let it happily fail
-    """
-    VERSIONFILE = os.path.join("src", PACKAGE, "__init__.py")
-    initfile_lines = open(VERSIONFILE, "rt").readlines()
-    VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
-    for line in initfile_lines:
-        mo = re.search(VSRE, line, re.M)
-        if mo:
-            return mo.group(1)
-
 
 setup(
     name=PACKAGE,
-    version=get_version(),
-    description="PDF set compressor",
-    author="Stefano Carrazza, Juan Cruz Martinez, Tanjona R. Rabemananjara",
+    version='1.0.0-dev',
+    description="PDF Compression",
+    long_description=LONG_DESCRIPTION,
+    long_description_content_type="text/markdown",
+    author="N3PDF",
     author_email="tanjona.rabemananjara@mi.infn.it",
+    license="GPL 3.0",
     url="https://github.com/N3PDF/pyCompressor",
-    extras_require={"docs": DOCS_REQUIEREMENTS, "tests": TESTS_REQUIEREMENTS},
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    install_requires=PACKAGE_REQUIEREMENTS,
-    entry_points={"console_scripts":
-        [
+    zip_safe=False,
+    project_urls={
+        "Documentation": "https://n3pdf.github.io/pycompressor/",
+        "Source": "https://github.com/N3PDF/pyCompressor"
+    },
+    entry_points={
+        "console_scripts": [
             "pycomp = pycompressor.scripts.main:main",
             "validate = pycompressor.scripts.validate:main",
             "cmp-fids = pycompressor.scripts.fids:main",
@@ -107,10 +59,12 @@ def get_version():
     },
     package_dir={"": "src"},
     packages=find_packages("src"),
+    install_requires=REQUIREMENTS,
     classifiers=[
         "Operating System :: Unix",
         "Programming Language :: Python",
         "Programming Language :: Python :: 3",
+        "Programming Language :: Python :: 3 :: Only",
         "Topic :: Scientific/Engineering",
         "Topic :: Scientific/Engineering :: Physics",
     ],

src/pycompressor/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.0.0-dev"

src/pycompressor/app.py

@@ -1,16 +1,13 @@
-# implement ValidPhys application
+# ValidPhys Action
 
-import re
 import sys
-import shutil
 import pathlib
 import logging
-import hashlib
 import warnings
 
-from validphys.app import App
 from reportengine import colors
 from reportengine.compat import yaml
+from validphys.app import App
 from validphys.config import Environment, Config
 from validphys.config import EnvironmentError_, ConfigError
 
@@ -34,9 +31,8 @@ def init_output(self):
         # check file exists, is a file, has extension.
         if not self.config_yml.exists():
             raise CompressorError("Invalid runcard. File not found.")
-        else:
-            if not self.config_yml.is_file():
-                raise CompressorError("Invalid runcard. Must be a file.")
+        if not self.config_yml.is_file():
+            raise CompressorError("Invalid runcard. Must be a file.")
         # Check if results folder exists
         self.output_path = pathlib.Path(self.output_path).absolute()
         try:

src/pycompressor/compressing.py

@@ -1,5 +1,4 @@
 import json
-import shutil
 import logging
 import pathlib
 import numpy as np
@@ -10,12 +9,13 @@
 from rich.style import Style
 from rich.console import Console
 from numpy.random import Generator, PCG64
+from reportengine.checks import CheckError
+from reportengine.checks import make_argcheck
+
 from pycompressor.pdfgrid import XGrid
 from pycompressor.pdfgrid import PdfSet
-from pycompressor.compressor import compress
-from pycompressor.utils import remap_index
+from pycompressor.compressor import Compress
 from pycompressor.utils import extract_index
-from pycompressor.utils import extract_estvalues
 
 console = Console()
 log = logging.getLogger(__name__)
@@ -44,19 +44,30 @@ def splash():
     console.print(logo)
 
 
+@make_argcheck
+def check_validity(pdfsetting, compressed, gans):
+    members = pdfsetting["pdf"].load().GetMembers()
+    if members < compressed:
+        if not gans["enhance"] and not pdfsetting["existing_enhanced"]:
+            raise CheckError(
+                    f" Cannot get {compressed} replicas from"
+                    f" {members} members if enhancing is not active.")
+
+
+@check_validity
 def compressing(pdfsetting, compressed, minimizer, est_dic, gans):
     """
     Action that performs the compression. The parameters
     for the compression are provided by a `runcard.yml`.
 
     Parameters
     ----------
-        pdf: str
-            pdf/PDF name
-        compressed: int
-            Size of the compressed set
-        est_dic: dict
-            Dictionary containing the list of estimators
+    pdf: str
+        pdf/PDF name
+    compressed: int
+        Size of the compressed set
+    est_dic: dict
+        Dictionary containing the list of estimators
     """
 
     pdf = str(pdfsetting["pdf"])
@@ -136,7 +147,7 @@ def compressing(pdfsetting, compressed, minimizer, est_dic, gans):
     console.print(table)
 
     # Init. Compressor class
-    comp = compress(
+    comp = Compress(
         prior,
         enhanced,
         est_dic,
@@ -152,7 +163,7 @@ def compressing(pdfsetting, compressed, minimizer, est_dic, gans):
     if minimizer == "genetic":
         # Run compressor using GA
         with trange(nb_iter) as iter_range:
-            for i in iter_range:
+            for _ in iter_range:
                 iter_range.set_description("Compression")
                 erf, index = comp.genetic_algorithm(nb_mut=5)
                 erf_list.append(erf)