diff --git a/.github/workflows/ci-cd-workflow.yml b/.github/workflows/ci-cd-workflow.yml new file mode 100644 index 0000000..2385d1f --- /dev/null +++ b/.github/workflows/ci-cd-workflow.yml @@ -0,0 +1,83 @@ +name: MESMER-OpenSCM Runner CI-CD +on: + push: + branches: + - main + tags: + - 'v*' + pull_request: + +jobs: + linting-and-docs: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: ["ubuntu-latest"] + python-version: [3.8] + + steps: + - name: Checkout repository + uses: actions/checkout@v2 + - name: Cache conda + uses: actions/cache@v2 + with: + path: ~/conda_pkgs_dir + key: + ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{ + hashFiles('environment.yml') }} + - name: Setup conda + uses: conda-incubator/setup-miniconda@v2.0.1 + with: + channels: conda-forge + channel-priority: strict + activate-environment: mesmer-openscmrunner-tests + auto-update-conda: false + python-version: ${{ matrix.python-version }} + - name: Conda info + shell: bash -l {0} + run: conda info + - name: Run format and linting tests + shell: bash -l {0} + # TODO: use make -B conda-environment when mesmer is available + run: | + which python + conda install black flake8 isort + black --exclude _version.py --check src tests setup.py + flake8 src tests setup.py + isort --check-only --quiet src tests setup.py + + build: + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: ["ubuntu-latest"] + python-version: [3.8] + + steps: + - name: Checkout repository + uses: actions/checkout@v2 + - name: Cache conda + uses: actions/cache@v2 + with: + path: ~/conda_pkgs_dir + key: + ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{ + hashFiles('environment.yml') }} + - name: Setup conda + uses: conda-incubator/setup-miniconda@v2.0.1 + with: + channels: conda-forge + channel-priority: strict + activate-environment: mesmer-openscmrunner-tests + auto-update-conda: false + python-version: ${{ matrix.python-version }} + - name: Conda info + shell: bash -l {0} + run: conda info + - name: Run tests + shell: bash -l {0} + # TDOO: use make -B test + run: | + which python + conda install pytest + pytest tests/test_source_file_headers.py diff --git a/AUTHORS b/AUTHORS new file mode 100644 index 0000000..2f27b55 --- /dev/null +++ b/AUTHORS @@ -0,0 +1,10 @@ +External contributors +===================== + +- Zebedee Nicholls (MESMER-OpenSCM Runner lead developer) + +ETH Zurich team +=============== + +- Lea Beusch (MESMER developer) +- Mathias Hauser (MESMER long-term maintainer) diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..810fce6 --- /dev/null +++ b/LICENSE @@ -0,0 +1,621 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS diff --git a/README.rst b/README.rst index 4505b6d..8faa162 100644 --- a/README.rst +++ b/README.rst @@ -1,4 +1,29 @@ MESMER-OpenSCM Runner ===================== -Coupling between MESMER and `OpenSCM-Runner `_. +Coupling between `MESMER `_ and `OpenSCM-Runner `_. + +.. sec-begin-license + +License +------- + +Copyright (c) 2021 MESMER-OpenSCM Runner contributors, listed in AUTHORS, and ETH Zurich. + +MESMER-OpenSCM Runner is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License (see `LICENSE `_), or +(at your option) any later version. + +MESMER-OpenSCM Runner is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . + +The full list of code contributors can be found in AUTHORS or at +`github.com/MESMER-group/mesmer-openscmrunner/graphs/contributors `_. + +.. sec-end-license diff --git a/setup.py b/setup.py index dd45f53..84db24a 100644 --- a/setup.py +++ b/setup.py @@ -20,17 +20,18 @@ AUTHORS = [ ("Zeb Nicholls", "zebedee.nicholls@climate-energy-college.org"), ("Lea Beusch", "lea.beusch@env.ethz.ch"), + ("Mathias Hauser", "mathias.hauser@env.ethz.ch"), ] -URL = "https://github.com/znicholls/mesmer-openscmrunner" +URL = "https://github.com/MESMER-group/mesmer-openscmrunner" PROJECT_URLS = { - "Bug Reports": "https://github.com/znicholls/mesmer-openscmrunner/issues", + "Bug Reports": "https://github.com/MESMER-group/mesmer-openscmrunner/issues", # "Documentation": "https://mesmer-openscmruner.readthedocs.io/en/latest", - "Source": "https://github.com/znicholls/mesmer-openscmrunner", + "Source": "https://github.com/MESMER-group/mesmer-openscmrunner", } -LICENSE = None # "3-Clause BSD License" +LICENSE = "GPLv3+" # I think this is the right short-hand... CLASSIFIERS = [ "Development Status :: 4 - Beta", - # "License :: OSI Approved :: BSD License", + "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", "Intended Audience :: Developers", "Operating System :: OS Independent", "Programming Language :: Python :: 3.7", @@ -41,8 +42,9 @@ REQUIREMENTS = [ # "mesmer", # once released "openscm-runner>=0.6", - "scmdata>=0.9,<0.10", #whilst running notebooks with rcmip phase 2 output - ] + "scmdata>=0.9,<0.10", # whilst running notebooks with rcmip phase 2 output + "xarray==0.17.0", # whilst running notebooks with rcmip phase 2 output +] REQUIREMENTS_TESTS = [ "codecov", "nbval", diff --git a/src/mesmer_openscmrunner/__init__.py b/src/mesmer_openscmrunner/__init__.py index e69de29..e9804ac 100644 --- a/src/mesmer_openscmrunner/__init__.py +++ b/src/mesmer_openscmrunner/__init__.py @@ -0,0 +1,3 @@ +# MESMER-OpenSCM Runner, land-climate dynamics group, S.I. Seneviratne +# Copyright (c) 2021 MESMER-OpenSCM Runner contributors, listed in AUTHORS, and ETH Zurich. +# Licensed under the GNU General Public License v3.0 or later; see LICENSE or https://www.gnu.org/licenses/ diff --git a/src/mesmer_openscmrunner/_version.py b/src/mesmer_openscmrunner/_version.py index adb2098..36429b2 100644 --- a/src/mesmer_openscmrunner/_version.py +++ b/src/mesmer_openscmrunner/_version.py @@ -1,4 +1,3 @@ - # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build diff --git a/src/mesmer_openscmrunner/draw_realisations/__init__.py b/src/mesmer_openscmrunner/draw_realisations/__init__.py index 24db205..afaae66 100644 --- a/src/mesmer_openscmrunner/draw_realisations/__init__.py +++ b/src/mesmer_openscmrunner/draw_realisations/__init__.py @@ -1,3 +1,7 @@ +# MESMER-OpenSCM Runner, land-climate dynamics group, S.I. Seneviratne +# Copyright (c) 2021 MESMER-OpenSCM Runner contributors, listed in AUTHORS, and ETH Zurich. +# Licensed under the GNU General Public License v3.0 or later; see LICENSE or https://www.gnu.org/licenses/ + import joblib import mesmer.create_emulations import xarray as xr @@ -47,9 +51,6 @@ def _draw_realisations_from_mesmer_file_and_openscm_output( ``openscm_hfds`` contains variables other than ``"Heat Uptake|Ocean"`` """ mesmer_bundle = joblib.load(mesmer_bundle_file) - import pdb - pdb.set_trace() - time_mesmer = mesmer_bundle["time"] gsat_scenarios = set(openscm_gsat.get_unique_meta("scenario")) hfds_scenarios = set(openscm_hfds.get_unique_meta("scenario")) @@ -76,8 +77,12 @@ def _draw_realisations_from_mesmer_file_and_openscm_output( scen_tas = _filter_and_assert_1d(scen_gsat.filter(year=hard_coded_scen_years)) openscm_hfds_for_mesmer_scen = openscm_hfds_for_mesmer.filter(scenario=scenario) - hist_hfds = _filter_and_assert_1d(openscm_hfds_for_mesmer_scen.filter(year=hard_coded_hist_years)) - scen_hfds = _filter_and_assert_1d(openscm_hfds_for_mesmer_scen.filter(year=hard_coded_scen_years)) + hist_hfds = _filter_and_assert_1d( + openscm_hfds_for_mesmer_scen.filter(year=hard_coded_hist_years) + ) + scen_hfds = _filter_and_assert_1d( + openscm_hfds_for_mesmer_scen.filter(year=hard_coded_scen_years) + ) # TODO: remove hard-coding and actually map up with what MESMER expects preds_lt_scenario = {} @@ -104,15 +109,13 @@ def _draw_realisations_from_mesmer_file_and_openscm_output( land_fractions=mesmer_bundle["land_fractions"], time={ "hist": scen_gsat.filter(year=hard_coded_hist_years)["year"].values, - scenario: scen_gsat.filter(year=hard_coded_scen_years)["year"].values + scenario: scen_gsat.filter(year=hard_coded_scen_years)["year"].values, }, ) - result_scenario = ( - result_scenario - .squeeze(dim="scenario", drop=True) - .expand_dims({"scenario": [scenario]}) - ) + result_scenario = result_scenario.squeeze( + dim="scenario", drop=True + ).expand_dims({"scenario": [scenario]}) out.append(result_scenario) out = xr.merge(out) diff --git a/tests/conftest.py b/tests/conftest.py index 026d089..0c43045 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,10 +1,34 @@ +# MESMER-OpenSCM Runner, land-climate dynamics group, S.I. Seneviratne +# Copyright (c) 2021 MESMER-OpenSCM Runner contributors, listed in AUTHORS, and ETH Zurich. +# Licensed under the GNU General Public License v3.0 or later; see LICENSE or https://www.gnu.org/licenses/ + import os.path import pytest -TEST_DATA_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "test-data") +REPO_ROOT_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..") +TEST_DATA_DIR = os.path.join(REPO_ROOT_DIR, "tests", "test-data") @pytest.fixture def test_data_dir(): return TEST_DATA_DIR + + +@pytest.fixture +def repo_root_dir(): + return REPO_ROOT_DIR + + +def pytest_addoption(parser): + parser.addoption( + "--update-copyright-notices", + action="store_true", + default=False, + help="Overwrite expected values", + ) + + +@pytest.fixture +def update_copyright_notices(request): + return request.config.getoption("--update-copyright-notices") diff --git a/tests/integration/test_create_realisations.py b/tests/integration/test_create_realisations.py index 5fe90b9..0b76c88 100644 --- a/tests/integration/test_create_realisations.py +++ b/tests/integration/test_create_realisations.py @@ -1,3 +1,7 @@ +# MESMER-OpenSCM Runner, land-climate dynamics group, S.I. Seneviratne +# Copyright (c) 2021 MESMER-OpenSCM Runner contributors, listed in AUTHORS, and ETH Zurich. +# Licensed under the GNU General Public License v3.0 or later; see LICENSE or https://www.gnu.org/licenses/ + import os.path import scmdata @@ -54,7 +58,9 @@ def test_create_realisations_from_pre_run_data(test_data_dir): assert set(result.data_vars) == {"tas"} assert set(result.dims) == {"realisation", "scenario", "z", "year"} - assert set(result["scenario"].values) == set(openscm_gsat.get_unique_meta("scenario")) + assert set(result["scenario"].values) == set( + openscm_gsat.get_unique_meta("scenario") + ) # make sure we can get onto a lat lon grid from what is saved result_reshaped = result.set_index(z=("lat", "lon")).unstack("z") @@ -67,7 +73,9 @@ def test_create_realisations_from_pre_run_data(test_data_dir): } -def test_create_realisations_from_pre_run_data_with_unrecognised_scenario_name(test_data_dir): +def test_create_realisations_from_pre_run_data_with_unrecognised_scenario_name( + test_data_dir, +): mesmer_bundle_file = os.path.join( test_data_dir, "mesmer-bundles", "test-generic-mesmer-bundle.pkl" ) @@ -112,7 +120,9 @@ def test_create_realisations_from_pre_run_data_with_unrecognised_scenario_name(t assert set(result.data_vars) == {"tas"} assert set(result.dims) == {"realisation", "scenario", "z", "year"} - assert set(result["scenario"].values) == set(openscm_gsat.get_unique_meta("scenario")) + assert set(result["scenario"].values) == set( + openscm_gsat.get_unique_meta("scenario") + ) # make sure we can get onto a lat lon grid from what is saved result_reshaped = result.set_index(z=("lat", "lon")).unstack("z") diff --git a/tests/test_source_file_headers.py b/tests/test_source_file_headers.py new file mode 100644 index 0000000..7be6649 --- /dev/null +++ b/tests/test_source_file_headers.py @@ -0,0 +1,50 @@ +# MESMER-OpenSCM Runner, land-climate dynamics group, S.I. Seneviratne +# Copyright (c) 2021 MESMER-OpenSCM Runner contributors, listed in AUTHORS, and ETH Zurich. +# Licensed under the GNU General Public License v3.0 or later; see LICENSE or https://www.gnu.org/licenses/ +import datetime +import glob +import os.path + +import pytest + +LICENSE_TEMPLATE = """# MESMER-OpenSCM Runner, land-climate dynamics group, S.I. Seneviratne +# Copyright (c) 2021{} MESMER-OpenSCM Runner contributors, listed in AUTHORS, and ETH Zurich. +# Licensed under the GNU General Public License v3.0 or later; see LICENSE or https://www.gnu.org/licenses/""" + + +EXCLUDE = ["_version.py"] + + +def test_source_code_headers(repo_root_dir, update_copyright_notices, n_lines=None): + n_lines = len(LICENSE_TEMPLATE.split("\n")) if n_lines is None else n_lines + + files_to_check = glob.glob( + os.path.join(repo_root_dir, "tests", "**", "*.py"), recursive=True + ) + glob.glob(os.path.join(repo_root_dir, "src", "**", "*.py"), recursive=True) + + files_to_check = [f for f in files_to_check if os.path.basename(f) not in EXCLUDE] + + now = datetime.datetime.now() + current_year = now.year + if current_year == 2021: + license_template = LICENSE_TEMPLATE.format("") + else: + license_template = LICENSE_TEMPLATE.format("-{}".format(current_year)) + + for f in files_to_check: + with open(f) as fh: + contents = fh.read() + + if not contents.startswith(license_template): + if update_copyright_notices: + contents = "\n".join(contents.split("\n")[n_lines:]) + contents = "{}\n\n{}".format(license_template, contents) + with open(f, "w") as fh: + fh.write(contents) + else: + raise ValueError( + "Update headers in source files (failing file: {})".format(f) + ) + + if update_copyright_notices: + pytest.skip("Updated copyright notices")