Add license

.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

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)

README.rst

@@ -1,4 +1,29 @@
 MESMER-OpenSCM Runner
 =====================
 
-Coupling between MESMER and `OpenSCM-Runner <https://github.com/openscm/openscm-runner>`_.
+Coupling between `MESMER <https://github.com/MESMER-group/mesmer>`_ and `OpenSCM-Runner <https://github.com/openscm/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 <https://github.com/openscm/scmdata/blob/master/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 <https://www.gnu.org/licenses/>.
+
+The full list of code contributors can be found in AUTHORS or at
+[github.com/znicholls/mesmer-openscmrunner/graphs/contributors](https://github.com/znicholls/mesmer-openscmrunner/graphs/contributors).
+
+.. sec-end-license

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"
 PROJECT_URLS = {
     "Bug Reports": "https://github.com/znicholls/mesmer-openscmrunner/issues",
     # "Documentation": "https://mesmer-openscmruner.readthedocs.io/en/latest",
     "Source": "https://github.com/znicholls/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",

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/

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

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)

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")

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")

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")