v2.0

.github/workflows/ci-cd-workflow.yml

@@ -18,8 +18,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dev dependencies
       run: |
-        pip install --upgrade pip
-        pip install -e .[dev] --use-feature=2020-resolver
+        pip install --upgrade --user pip wheel
+        pip install -e .[dev]
     # TODO: add `pylint pymagicc`
     # TODO: add pydocstyle pymagicc
     - name: Formatting and linters
@@ -86,11 +86,18 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-pip-
 
+    # no windows wheel for Python 3.6 cftime 1.3.1
+    # https://github.com/Unidata/cftime/issues/224
+    - name: Install cftime 1.3.0 (${{ runner.os }})
+      if: startsWith(runner.os, 'Windows') && endsWith(matrix.python-version, '3.6')
+      run: |
+        pip install --upgrade --user pip wheel
+        pip install cftime==1.3.0
 
     - name: Install test dependencies
       run: |
-        pip install --upgrade pip
-        pip install -e .[tests] --use-feature=2020-resolver
+        pip install --upgrade --user pip wheel
+        pip install -e .[tests]
 
 
     - name: Test with pytest (${{ runner.os }})
@@ -111,6 +118,10 @@ jobs:
       run: |
           pytest tests -r a
 
+    - name: Test scripts (${{ runner.os }})
+      run: |
+          python scripts/plot_example.py
+
 
     - name: Upload coverage to Codecov
       if: startsWith(runner.os, 'Linux') && ${{ matrix.python-version }} == 3.7
@@ -158,10 +169,18 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-notebooks-pip-
 
+    # no windows wheel for Python 3.6 cftime 1.3.1
+    # https://github.com/Unidata/cftime/issues/224
+    - name: Install cftime 1.3.0 (${{ runner.os }})
+      if: startsWith(runner.os, 'Windows') && endsWith(matrix.python-version, '3.6')
+      run: |
+        pip install --upgrade --user pip wheel
+        pip install cftime==1.3.0
+
     - name: Install notebook dependencies
       run: |
-        pip install --upgrade pip
-        pip install -e .[tests,notebooks] --use-feature=2020-resolver
+        pip install --upgrade --user pip wheel
+        pip install -e .[tests,notebooks]
     - name: Test notebooks with nbval
       if: startsWith(runner.os, 'Linux')
       run: |
@@ -171,8 +190,40 @@ jobs:
       run: |
         pytest notebooks -r a --nbval --sanitize-with tests/notebook-tests.cfg --no-cov
 
+  test-install:
+    needs: build
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "windows-latest"]
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+    - name: Setup python
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    # no windows wheel for Python 3.6 cftime 1.3.1
+    # https://github.com/Unidata/cftime/issues/224
+    - name: Install cftime 1.3.0 (${{ runner.os }})
+      if: startsWith(runner.os, 'Windows') && endsWith(matrix.python-version, '3.6')
+      run: |
+        pip install --upgrade --user pip wheel
+        pip install cftime==1.3.0
+
+    - name: Install (${{ runner.os }})
+      run: |
+        pip install --upgrade pip wheel
+        pip install .
+    - name: Test installation
+      run: |
+          python scripts/test_install.py
+
   deploy-pypi:
-    needs: test-notebooks
+    needs: [test-notebooks,test-install]
     if: startsWith(github.ref, 'refs/tags/v')
 
     runs-on: ubuntu-latest
@@ -189,8 +240,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        pip install --upgrade pip
-        pip install -e .[dev] --use-feature=2020-resolver
+        pip install --upgrade --user pip wheel
+        pip install -e .[dev]
     - name: Create package
       run: python setup.py sdist bdist_wheel --universal
     - name: Publish package to PyPI

README.rst

@@ -91,28 +91,25 @@ Basic Usage
     import matplotlib.pyplot as plt
 
     import pymagicc
-    from pymagicc import scenarios
+    import scmdata
+    from pymagicc import rcps
 
-    for name, scen in scenarios.items():
-        results = pymagicc.run(scen)
-        results_df = results.df
-        results_df.set_index("time", inplace=True)
+    results = []
+    for scen in rcps.groupby("scenario"):
+        results_scen = pymagicc.run(scen)
+        results.append(results_scen)
 
-        global_temp_time_rows = (
-            (results_df.variable == "Surface Temperature")
-            & (results_df.region == "World")
-        )
+    results = scmdata.run_append(results)
 
-        temp = (
-            results_df.value[global_temp_time_rows].loc[1850:]
-            - results_df.value[global_temp_time_rows].loc[1850:1900].mean()
-        )
-        temp.plot(label=name)
+    temperature_rel_to_1850_1900 = (
+        results
+        .filter(variable="Surface Temperature", region="World")
+        .relative_to_ref_period_mean(year=range(1850, 1900 + 1))
+    )
 
-    plt.legend()
+    temperature_rel_to_1850_1900.lineplot()
     plt.title("Global Mean Temperature Projection")
     plt.ylabel("°C over pre-industrial (1850-1900 mean)");
-    plt.legend(loc="best")
     # Run `plt.show()` to display the plot when running this example
     # interactively or add `%matplotlib inline` on top when in a Jupyter Notebook.
 
@@ -266,16 +263,16 @@ Use an included scenario
 
 .. code:: python
 
-    from pymagicc import rcp26
+    from pymagicc.scenarios import rcp26
 
-    rcp26.df.head()
+    rcp26.head()
 
 Read a MAGICC scenario file
 ***************************
 
 .. code:: python
 
-    from pymagicc import read_scen_file
+    from pymagicc.scenarios import read_scen_file
 
     scenario = read_scen_file("PATHWAY.SCEN")
 
@@ -284,18 +281,17 @@ Run MAGICC for a scenario
 
 .. code:: python
 
-    results = pymagicc.run(scenario)
-    results_df = results.df
-    results_df.set_index("time", inplace=True)
+    import pymagicc
+    from pymagicc.scenarios import read_scen_file
 
-    global_temp_time_rows = (
-        (results_df.variable == "Surface Temperature")
-        & (results_df.region == "World")
-    )
+    scenario = read_scen_file("PATHWAY.SCEN")
+
+    results = pymagicc.run(scenario)
 
-    temp = (
-        results_df.value[global_temp_time_rows].loc[1850:]
-        - results_df.value[global_temp_time_rows].loc[1850:1900].mean()
+    temperature_rel_to_1850_1900 = (
+        results
+        .filter(variable="Surface Temperature")
+        .relative_to_ref_period_mean(year=range(1850, 1900 + 1))
     )
 
 Using a different MAGICC version

pymagicc/io/base.py

@@ -743,10 +743,20 @@ def _ensure_file_region_type_consistency(self, regions):
         # no checks required except for certain cases
         return regions
 
-    def _get_data_block(self):
-        data_block = self.minput.timeseries(
+    def _get_timeseries_no_nans(self):
+        out = self.minput.timeseries(
             meta=["variable", "todo", "unit", "region"]
-        ).T
+        ).T.dropna(how="all")
+        if out.isnull().any().any():
+            raise AssertionError(
+                "Your data contains timesteps where some values are nan whilst others "
+                "are not. This will not work in MAGICC."
+            )
+
+        return out
+
+    def _get_data_block(self):
+        data_block = self._get_timeseries_no_nans()
         self._check_data_block_column_names(data_block)
         self._check_data_filename_variable_consistency(data_block)
 

pymagicc/io/prn_files.py

@@ -255,9 +255,7 @@ def _get_unit(self):
         return unit
 
     def _get_data_block(self):
-        data_block = self.minput.timeseries(
-            meta=["variable", "todo", "unit", "region"]
-        ).T
+        data_block = self._get_timeseries_no_nans()
         self._check_data_block_column_names(data_block)
 
         regions = data_block.columns.get_level_values("region").unique()

pymagicc/scenarios/__init__.py

@@ -62,7 +62,7 @@ def read_scen_file(
 
 rcps = deepcopy(rcp26)
 for rcp in [rcp45, rcp60, rcp85]:
-    rcps.append(rcp)
+    rcps = rcps.append(rcp)
 
 zero_emissions = MAGICCData(
     join(dirname(abspath(__file__)), "RCP3PD_EMISSIONS.DAT"),

scripts/plot_example.py

@@ -1,9 +1,9 @@
 import os
-import matplotlib.pyplot as plt
-
 
+import matplotlib.pyplot as plt
 import pymagicc
-from pymagicc import scenarios
+import scmdata
+from pymagicc import rcps
 
 
 plt.style.use("ggplot")
@@ -17,25 +17,21 @@
     './example-plot.png'
 )
 
-for name, scen in scenarios.items():
-    results = pymagicc.run(scen)
-    results_df = results.df
-    results_df.set_index("time", inplace=True)
+results = []
+for scen in rcps.groupby("scenario"):
+    results_scen = pymagicc.run(scen)
+    results.append(results_scen)
 
-    global_temp_time_rows = (
-        (results_df.variable == "Surface Temperature")
-        & (results_df.region == "World")
-    )
+results = scmdata.run_append(results)
 
-    temp = (
-        results_df.value[global_temp_time_rows].loc[1850:]
-        - results_df.value[global_temp_time_rows].loc[1850:1900].mean()
-    )
-    temp.plot(label=name)
+temperature_rel_to_1850_1900 = (
+    results
+    .filter(variable="Surface Temperature", region="World")
+    .relative_to_ref_period_mean(year=range(1850, 1900 + 1))
+)
 
-plt.legend()
+temperature_rel_to_1850_1900.lineplot()
 plt.title("Global Mean Temperature Projection")
-plt.ylabel("°C over pre-industrial (1850-1900 mean)");
-plt.legend(loc="best")
+plt.ylabel("°C over pre-industrial (1850-1900 mean)")
 
 plt.savefig(output_path, dpi=96)

setup.py

@@ -46,6 +46,7 @@
     "Programming Language :: Python :: 3.8",
 ]
 REQUIREMENTS_INSTALL = [
+    "cftime",
     "pandas-datapackage-reader",
     "f90nml",
     "PyYAML",
@@ -67,6 +68,7 @@
     "codecov",
     "goodtables",
     "scipy",
+    "seaborn",
 ]
 REQUIREMENTS_DOCS = [
     "sphinx>2.1",

tests/test_io.py

@@ -2907,7 +2907,7 @@ def test_conc_in_reader_get_variable_from_filepath(test_filepath, expected_varia
         assert conc_reader._get_variable_from_filepath() == expected_variable
 
 
-@pytest.mark.parametrize(
+ALL_FILE_TYPES = pytest.mark.parametrize(
     "magicc_version, starting_fpath, starting_fname, confusing_metadata, old_namelist",
     [
         (6, MAGICC6_DIR, "HISTRCP_CO2I_EMIS.IN", False, False),
@@ -2953,6 +2953,9 @@ def test_conc_in_reader_get_variable_from_filepath(test_filepath, expected_varia
         (7, TEST_DATA_DIR, "MAG_FORMAT_SAMPLE_TWO.MAG", False, False),
     ],
 )
+
+
+@ALL_FILE_TYPES
 def test_in_file_read_write_functionally_identical(
     magicc_version,
     starting_fpath,
@@ -2993,6 +2996,56 @@ def test_in_file_read_write_functionally_identical(
     )
 
 
+@ALL_FILE_TYPES
+def test_nans_stripped_before_writing(
+    magicc_version,
+    starting_fpath,
+    starting_fname,
+    confusing_metadata,
+    old_namelist,
+    temp_dir,
+):
+    mi_writer = MAGICCData(join(starting_fpath, starting_fname))
+
+    nan_idx = mi_writer.shape[1] // 2
+    nan_timestep = mi_writer["time"].iloc[nan_idx]
+
+    assert nan_timestep in mi_writer["time"].values
+
+    mi_writer.values[:, nan_idx] = np.nan
+
+    mi_writer.write(join(temp_dir, starting_fname), magicc_version=magicc_version)
+
+    mi_written = MAGICCData(join(temp_dir, starting_fname))
+    assert nan_timestep not in mi_written["time"].values
+
+
+@ALL_FILE_TYPES
+def test_raises_if_nans_not_uniform(
+    magicc_version,
+    starting_fpath,
+    starting_fname,
+    confusing_metadata,
+    old_namelist,
+    temp_dir,
+):
+    mi_writer = MAGICCData(join(starting_fpath, starting_fname))
+
+    if mi_writer.shape[0] == 1:
+        pytest.skip("Only one timeseries so can't create mismatch")
+
+    nan_row = mi_writer.shape[0] // 2
+    nan_col = mi_writer.shape[1] // 2
+    mi_writer.values[nan_row, nan_col] = np.nan
+
+    error_msg = re.escape(
+        "Your data contains timesteps where some values are nan whilst others "
+        "are not. This will not work in MAGICC."
+    )
+    with pytest.raises(AssertionError, match=error_msg):
+        mi_writer.write(join(temp_dir, starting_fname), magicc_version=magicc_version)
+
+
 emissions_valid = [
     "CO2I",
     "CO2B",