diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index d7a9374c..3fa0ce28 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -33,12 +33,11 @@ jobs: run: | sudo apt install libimage-exiftool-perl -y sudo apt-get install -y netcdf-bin - - name: Install dependencies + - name: Install dependencies and checksit run: | python -m pip install --upgrade pip pip install flake8 black pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - if [ -f requirements_dev.txt ]; then pip install -r requirements_dev.txt; fi + pip install '.[dev]' - name: Test with pytest run: | export UDUNITS2_XML_PATH=/opt/share/udunits/udunits2.xml diff --git a/LICENSE b/LICENSE index d65dae27..d781e9df 100644 --- a/LICENSE +++ b/LICENSE @@ -1,4 +1,4 @@ -Copyright 2020 United Kingdom Research and Innovation +Copyright 2025 United Kingdom Research and Innovation Authors: Ag Stephens @@ -23,4 +23,4 @@ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE -POSSIBILITY OF SUCH DAMAGE. +POSSIBILITY OF SUCH DAMAGE. \ No newline at end of file diff --git a/checksit/config.py b/checksit/config.py index d96405a6..d0b843b8 100644 --- a/checksit/config.py +++ b/checksit/config.py @@ -1,6 +1,17 @@ import os from configparser import ConfigParser from itertools import chain +import sys + +if sys.version_info >= (3, 9): + from importlib.resources import files +else: + from importlib_resources import files as imported_files + def files(package): + return imported_files(package) + + +PACKAGE_ROOT = files("checksit") # Global CONFIG used by other packages _CONFIG = None @@ -19,7 +30,8 @@ def get_config(package=None): def _gather_config_files(package=None): conf_files = [] - _config = os.path.join(os.path.dirname(__file__), "etc", ini_file) + #_config = os.path.join(os.path.dirname(__file__), "etc", ini_file) + _config = os.path.join(str(PACKAGE_ROOT), "etc", ini_file) if not os.path.isfile(_config): print(f"[WARN] Cannot load default config file from: {_config}") @@ -101,6 +113,7 @@ def _load_config(package=None): conf = ConfigParser() conf.read(conf_files) + conf["settings"].update({'basedir': str(PACKAGE_ROOT)}) config = {} mappers = _get_mappers(conf) diff --git a/specs/groups/ceda-base.yml b/checksit/data/specs/groups/ceda-base.yml similarity index 100% rename from specs/groups/ceda-base.yml rename to checksit/data/specs/groups/ceda-base.yml diff --git a/specs/groups/esa-cci-v1.0/esa-cci-file-name-add-seg.yml b/checksit/data/specs/groups/esa-cci-v1.0/esa-cci-file-name-add-seg.yml similarity index 100% rename from specs/groups/esa-cci-v1.0/esa-cci-file-name-add-seg.yml rename to checksit/data/specs/groups/esa-cci-v1.0/esa-cci-file-name-add-seg.yml diff --git a/specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-add-seg-gds.yml b/checksit/data/specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-add-seg-gds.yml similarity index 100% rename from specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-add-seg-gds.yml rename to checksit/data/specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-add-seg-gds.yml diff --git a/specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-add-seg.yml b/checksit/data/specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-add-seg.yml similarity index 100% rename from specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-add-seg.yml rename to checksit/data/specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-add-seg.yml diff --git a/specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-gds.yml b/checksit/data/specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-gds.yml similarity index 100% rename from specs/groups/esa-cci-v1.0/esa-cci-file-name-ghrsst-gds.yml rename to 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a/specs/groups/ncas-amof-1.0.0/amof-depolarisation-ratio.yml b/checksit/data/specs/groups/ncas-amof-1.0.0/amof-depolarisation-ratio.yml similarity index 100% rename from specs/groups/ncas-amof-1.0.0/amof-depolarisation-ratio.yml rename to checksit/data/specs/groups/ncas-amof-1.0.0/amof-depolarisation-ratio.yml diff --git a/specs/groups/ncas-amof-1.0.0/amof-dew-point.yml b/checksit/data/specs/groups/ncas-amof-1.0.0/amof-dew-point.yml similarity index 100% rename from specs/groups/ncas-amof-1.0.0/amof-dew-point.yml rename to checksit/data/specs/groups/ncas-amof-1.0.0/amof-dew-point.yml diff --git a/specs/groups/ncas-amof-1.0.0/amof-file-name.yml b/checksit/data/specs/groups/ncas-amof-1.0.0/amof-file-name.yml similarity index 100% rename from specs/groups/ncas-amof-1.0.0/amof-file-name.yml rename to checksit/data/specs/groups/ncas-amof-1.0.0/amof-file-name.yml diff --git a/specs/groups/ncas-amof-1.0.0/amof-flux-components.yml 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a/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_ann_198012-200011.cdl b/checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_ann_198012-200011.cdl similarity index 100% rename from template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_ann_198012-200011.cdl rename to checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_ann_198012-200011.cdl diff --git a/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_day_19801201-19901130.cdl b/checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_day_19801201-19901130.cdl similarity index 100% rename from template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_day_19801201-19901130.cdl rename to checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_day_19801201-19901130.cdl diff --git a/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_mon-20y_198012-200011.cdl b/checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_mon-20y_198012-200011.cdl similarity index 100% rename from template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_mon-20y_198012-200011.cdl rename to checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_mon-20y_198012-200011.cdl diff --git a/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_mon_198012-200011.cdl b/checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_mon_198012-200011.cdl similarity index 100% rename from template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_mon_198012-200011.cdl rename to checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_mon_198012-200011.cdl diff --git a/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_seas-20y_198012-200011.cdl b/checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_seas-20y_198012-200011.cdl similarity index 100% rename from template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_seas-20y_198012-200011.cdl rename to checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_seas-20y_198012-200011.cdl diff --git a/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_seas_198012-200011.cdl b/checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_seas_198012-200011.cdl similarity index 100% rename from template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_seas_198012-200011.cdl rename to checksit/data/template-cache/wsgmax10m_rcp85_land-cpm_uk_river_01_seas_198012-200011.cdl diff --git a/checksit/etc/checksit.ini b/checksit/etc/checksit.ini index 3ec999aa..a6b00542 100644 --- a/checksit/etc/checksit.ini +++ b/checksit/etc/checksit.ini @@ -5,7 +5,7 @@ lists = excludes extra_lists = dicts = extra_dicts = -booleans = +booleans = extra_booleans = ints = extra_ints = @@ -14,17 +14,17 @@ extra_floats = [settings] basedir = . -vocabs_dir = %(basedir)s/checksit/vocabs +vocabs_dir = %(basedir)s/vocabs vocabs_prefix = __vocabs__ rules_prefix = __rules__ rule_splitter = | -format_checks_dir = $(basedir)s/checksit/fmt_checks -excludes = +format_checks_dir = %(basedir)s/fmt_checks +excludes = #global_attributes:creation_date global_attributes:version -default_template_cache_dir = template-cache +default_template_cache_dir = %(basedir)stemplate-cache template_cache_dirs = template-cache other-cache default_template = template-cache/ceda-base.yml -specs_dir = %(basedir)s/specs +specs_dir = %(basedir)s/data/specs [dataset:ukmo-assim] regex_file = ukmo-nwp-strat_gbl-std_\d{10}_u-v-gph-t-w\.pp diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 00000000..3f0162e2 --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,81 @@ +[build-system] +requires = ["setuptools", "setuptools-scm"] +build-backend = "setuptools.build_meta" + +[project] +name = "checksit" +authors = [ + {name = "Ag Stephens", email = "ag.stephens@stfc.ac.uk"}, +] +description = "File checking made simple" +readme = "README.md" +requires-python = ">=3.7" +license = {"text" = "BSD-3-Clause"} +classifiers = [ + "Development Status :: 5 - Production/Stable", + "Environment :: Console", + "Environment :: Web Environment", + "Intended Audience :: End Users/Desktop", + "Intended Audience :: Developers", + "Intended Audience :: System Administrators", + "Intended Audience :: Science/Research", + "Natural Language :: English", + "Operating System :: Microsoft :: Windows", + "Operating System :: POSIX :: Linux", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", + "Topic :: Scientific/Engineering", + "Topic :: Software Development :: Libraries :: Python Modules", +] +dependencies = [ + "click", + "pyyaml", + "cf-python", + "netcdf4", + "pandas", + "requests", + "numpy", + "importlib-resources ; python_version < '3.9'", +] +keywords = [ + "checksit", + "file check", + "CEDA", + "Centre for Environmental Data Analysis", +] +dynamic = ["version"] + +[project.optional-dependencies] +dev = [ + "pytest", + "build", +] +docs = [ + "sphinx", + "sphinx-rtd-theme", +] + +[project.scripts] +checksit = "checksit.cli:main" + +[project.urls] +Homepage = "https://github.com/cedadev/checksit" +Documentation = "https://checksit.readthedocs.io" +Repository = "https://github.com/cedadev/checksit" + +[tool.setuptools.dynamic] +version = {attr = "checksit.__version__"} + +[tool.setuptools.packages.find] +include = ["checksit*"] + +[tool.setuptools.package-data] +"checksit" = ["data/*"] diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 7c9b8933..00000000 --- a/requirements.txt +++ /dev/null @@ -1,7 +0,0 @@ -click -pyyaml -cf-python -netcdf4 -pandas -requests -numpy diff --git a/requirements_dev.txt b/requirements_dev.txt deleted file mode 100644 index 6c3a449a..00000000 --- a/requirements_dev.txt +++ /dev/null @@ -1,14 +0,0 @@ -pip -bump2version -wheel -watchdog -flake8 -tox -coverage -Sphinx -twine -pre-commit -Click -pytest -pytest-runner -deepdiff diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 4f6b2bc4..00000000 --- a/setup.cfg +++ /dev/null @@ -1,19 +0,0 @@ -[bdist_wheel] -universal = 1 - -[flake8] -exclude = - .git, - docs, - build, - .eggs, -max-line-length = 88 -max-complexity = 12 - -[aliases] -# Define setup.py command aliases here -test = pytest - -[tool:pytest] -collect_ignore = ['setup.py'] - diff --git a/setup.py b/setup.py deleted file mode 100644 index 9fa8be5d..00000000 --- a/setup.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python - -"""The setup script.""" - -from setuptools import setup, find_packages -from checksit import __version__ - -__author__ = "Ag Stephens" -__contact__ = "ag.stephens@stfc.ac.uk" -__copyright__ = "Copyright 2020 United Kingdom Research and Innovation" -__license__ = "BSD - see LICENSE file in top-level package directory" - -with open('README.md') as readme_file: - readme = readme_file.read() - -with open('HISTORY.rst') as history_file: - history = history_file.read() - -requirements = [line.strip() for line in open("requirements.txt")] - -dev_requirements = [line.strip() for line in open("requirements_dev.txt")] - -test_requirements = ['pytest>=3', ] - -docs_requirements = [ - "sphinx", - "sphinx-rtd-theme", - "nbsphinx", - "pandoc", - "ipython", - "ipykernel", - "jupyter_client" -] - -setup( - author=__author__, - author_email=__contact__, - python_requires='>=3.6', - setup_requires = ['setuptools_scm'], -# use_scm_version=True, - version=__version__, - classifiers=[ - 'Development Status :: 5 - Production/Stable', - 'Environment :: Console', - 'Environment :: Web Environment', - 'Intended Audience :: End Users/Desktop', - 'Intended Audience :: Developers', - 'Intended Audience :: System Administrators', - 'Intended Audience :: Science/Research', - 'License :: OSI Approved :: BSD License', - 'Natural Language :: English', - 'Operating System :: Microsoft :: Windows', - 'Operating System :: POSIX :: Linux', - 'Programming Language :: Python', - 'Programming Language :: Python :: 3', - 'Programming Language :: Python :: 3.5', - 'Programming Language :: Python :: 3.6', - 'Programming Language :: Python :: 3.7', - 'Programming Language :: Python :: 3.8', - 'Topic :: Security', - 'Topic :: Internet', - 'Topic :: Scientific/Engineering', - 'Topic :: System :: Distributed Computing', - 'Topic :: System :: Systems Administration :: Authentication/Directory', - 'Topic :: Software Development :: Libraries :: Python Modules' - ], - description="File checking made simple", - entry_points={ - 'console_scripts': [ - 'checksit=checksit.cli:main', - ], - }, - install_requires=requirements, - license=__license__, - long_description=readme, - long_description_content_type="text/x-rst", - include_package_data=True, - keywords='checksit', - name='checksit', - packages=find_packages(include=['checksit', 'checksit.*']), - test_suite='tests', - tests_require=test_requirements, - extras_require={"docs": docs_requirements, - "dev": dev_requirements}, - url='https://github.com/cedadev/checksit', - zip_safe=False, -)