Merge branch 'main' of github.com:NCAS-CMS/cf-python into ugrid-0

Changelog.rst

@@ -1,3 +1,11 @@
+version 3.15.3
+--------------
+
+**2023-08-31**
+
+* Prevent unlimited dimensions from being written to CFA-netCDF files
+  (https://github.com/NCAS-CMS/cf-python/issues/689)
+
 version 3.15.2
 --------------
 

DOCUMENTATION.md

@@ -8,6 +8,9 @@
   sphinxcontrib-spelling==4.3.0
 
 * The `.py` files to generate recipes are stored in `docs/source/recipes/`.
+  
+* The netCDF and PP files for generation of the same are available to download at: 
+  https://drive.google.com/drive/folders/1gaMHbV0A37hzQHH_C5oMBWOoxgoQPdCT?usp=sharing
 
 * For every new added recipe, `docs/source/recipes/recipe_list.txt` has to be
   edited to include the newly added recipe with its corresponding filters in the

RELEASE.md

@@ -164,3 +164,5 @@
   https://github.com/NCAS-CMS/cf-python/releases
 
 * Upload the new release to Zenodo: https://zenodo.org/record/3961353
+
+* Copy the archive docs to https://github.com/NCAS-CMS/cf-python-docs

cf/__init__.py

@@ -74,8 +74,8 @@
 """
 
 __Conventions__ = "CF-1.10"
-__date__ = "2023-07-21"
-__version__ = "3.15.2"
+__date__ = "2023-08-31"
+__version__ = "3.15.3"
 
 _requires = (
     "numpy",
@@ -193,7 +193,7 @@
     )
 
 # Check the version of cfdm
-_minimum_vn = "1.10.1.1"
+_minimum_vn = "1.10.1.2"
 _maximum_vn = "1.10.2.0"
 _cfdm_version = Version(cfdm.__version__)
 if not Version(_minimum_vn) <= _cfdm_version < Version(_maximum_vn):

cf/read_write/netcdf/netcdfwrite.py

@@ -22,6 +22,32 @@ def __new__(cls, *args, **kwargs):
         instance._NetCDFRead = NetCDFRead
         return instance
 
+    def _unlimited(self, field, axis):
+        """Whether an axis is unlimited.
+
+        If a CFA-netCDF file is being written then no axis can be
+        unlimited, i.e. `False` is always returned.
+
+        .. versionadded:: 3.15.3
+
+        :Parameters:
+
+            field: `Field` or `Domain`
+
+            axis: `str`
+                Domain axis construct identifier,
+                e.g. ``'domainaxis1'``.
+
+        :Returns:
+
+            `bool`
+
+        """
+        if self.write_vars["cfa"]:
+            return False
+
+        return super()._unlimited(field, axis)
+
     def _write_as_cfa(self, cfvar, construct_type, domain_axes):
         """Whether or not to write as a CFA variable.
 

cf/test/test_CFA.py

@@ -435,8 +435,6 @@ def test_CFA_PP(self):
 
     def test_CFA_multiple_files(self):
         """Test storing multiple CFA frgament locations."""
-        tmpfile1 = "delme1.nc"
-        tmpfile2 = "delme2.nc"
         f = cf.example_field(0)
         cf.write(f, tmpfile1)
         f = cf.read(tmpfile1)[0]
@@ -451,6 +449,22 @@ def test_CFA_multiple_files(self):
         self.assertEqual(len(g.data.get_filenames()), 2)
         self.assertEqual(len(g.get_filenames()), 3)
 
+    def test_CFA_unlimited_dimension(self):
+        """Test CFA with unlimited dimensions"""
+        # Create a CFA file from a field that has an unlimited
+        # dimension and no metadata constructs spanning that dimension
+        f = cf.example_field(0)
+        d = f.domain_axis("X")
+        d.nc_set_unlimited(True)
+        f.del_construct("X")
+        cf.write(f, tmpfile1)
+        g = cf.read(tmpfile1)
+        cf.write(g, tmpfile2, cfa=True)
+
+        # Check that the CFA file can be read
+        h = cf.read(tmpfile2)
+        self.assertEqual(len(h), 1)
+
 
 if __name__ == "__main__":
     print("Run date:", datetime.datetime.now())

docs/2_to_3_changes.html

@@ -24,6 +24,7 @@
     <script src="_static/copybutton.js"></script>
     <script src="_static/toggleprompt.js"></script>
     <script async="async" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="shortcut icon" href="_static/favicon.ico"/>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
 
@@ -37,10 +38,13 @@
 
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
         <div class="sphinxsidebarwrapper">
+            <p class="logo"><a href="index.html">
+              <img class="logo" src="_static/logo.svg" alt="Logo"/>
+            </a></p>
 
 
 
-<h1 class="logo"><a href="index.html">cf 3.15.2</a></h1>
+<h1 class="logo"><a href="index.html">cf 3.15.3</a></h1>
 
 
 
@@ -487,7 +491,7 @@ <h2>Changes to the  API of existing methods<a class="headerlink" href="#changes-
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;2023, NCAS | Page built on 2023-07-21.
+      &copy;2023, NCAS | Page built on 2023-08-31.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 2.4.5</a>

docs/_downloads/plot_01_recipe.ipynb

@@ -219,7 +219,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_02_recipe.ipynb

@@ -266,7 +266,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_03_recipe.ipynb

@@ -125,7 +125,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_04_recipe.ipynb

@@ -129,7 +129,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_05_recipe.ipynb

@@ -151,7 +151,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_06_recipe.ipynb

@@ -197,7 +197,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_07_recipe.ipynb

@@ -143,7 +143,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_08_recipe.ipynb

@@ -204,7 +204,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_09_recipe.ipynb

@@ -226,7 +226,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_10_recipe.ipynb

@@ -176,7 +176,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_11_recipe.ipynb

@@ -226,7 +226,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_12_recipe.ipynb

@@ -166,7 +166,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "9. Now plot both the AOD from `high-quality` retrieval and all other retrievals \nusing [cfplot.con](http://ajheaps.github.io/cf-plot/con.html). Here:\n\n- [cfplot.gopen](http://ajheaps.github.io/cf-plot/gopen.html) is used to \n  define the parts of the plot area, specifying that the figure should have \n  1 row and 2 columns, which is closed by \n  [cfplot.gclose](http://ajheaps.github.io/cf-plot/gclose.html);\n- [plt.suptitle](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.suptitle.html)\n  is used to add a title for the whole figure;\n- the subplots for plotting are selected using \n  [cfplot.gpos](https://ajheaps.github.io/cf-plot/gpos.html) after which \n  [cfplot.mapset](https://ajheaps.github.io/cf-plot/mapset.html) is used to \n  set the map limits and resolution for the subplots;  \n- and as cf-plot stores the plot in a plot object with the name \n  ``cfp.plotvars.plot``, country borders are added using normal \n  [Cartopy operations](https://scitools.org.uk/cartopy/docs/latest/reference/index.html) \n  on the ``cfp.plotvars.mymap`` object:\n\n"
+        "9. Now plot both the AOD from `high-quality` retrieval and all other retrievals\nusing [cfplot.con](http://ajheaps.github.io/cf-plot/con.html). Here:\n\n- [cfplot.gopen](http://ajheaps.github.io/cf-plot/gopen.html) is used to\n  define the parts of the plot area, specifying that the figure should have\n  1 row and 2 columns, which is closed by\n  [cfplot.gclose](http://ajheaps.github.io/cf-plot/gclose.html);\n- [plt.suptitle](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.suptitle.html)\n  is used to add a title for the whole figure;\n- the subplots for plotting are selected using\n  [cfplot.gpos](https://ajheaps.github.io/cf-plot/gpos.html) after which\n  [cfplot.mapset](https://ajheaps.github.io/cf-plot/mapset.html) is used to\n  set the map limits and resolution for the subplots;\n- and as cf-plot stores the plot in a plot object with the name\n  ``cfp.plotvars.plot``, country borders are added using normal\n  [Cartopy operations](https://scitools.org.uk/cartopy/docs/latest/reference/index.html)\n  on the ``cfp.plotvars.mymap`` object:\n\n"
       ]
     },
     {
@@ -197,7 +197,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_12_recipe.py

@@ -67,22 +67,22 @@
 high = aod.where(mask, cf.masked)
 
 # %%
-# 9. Now plot both the AOD from `high-quality` retrieval and all other retrievals 
+# 9. Now plot both the AOD from `high-quality` retrieval and all other retrievals
 # using `cfplot.con <http://ajheaps.github.io/cf-plot/con.html>`_. Here:
 #
-# - `cfplot.gopen <http://ajheaps.github.io/cf-plot/gopen.html>`_ is used to 
-#   define the parts of the plot area, specifying that the figure should have 
-#   1 row and 2 columns, which is closed by 
+# - `cfplot.gopen <http://ajheaps.github.io/cf-plot/gopen.html>`_ is used to
+#   define the parts of the plot area, specifying that the figure should have
+#   1 row and 2 columns, which is closed by
 #   `cfplot.gclose <http://ajheaps.github.io/cf-plot/gclose.html>`_;
 # - `plt.suptitle <https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.suptitle.html>`_
 #   is used to add a title for the whole figure;
-# - the subplots for plotting are selected using 
-#   `cfplot.gpos <https://ajheaps.github.io/cf-plot/gpos.html>`_ after which 
-#   `cfplot.mapset <https://ajheaps.github.io/cf-plot/mapset.html>`_ is used to 
-#   set the map limits and resolution for the subplots;  
-# - and as cf-plot stores the plot in a plot object with the name 
-#   ``cfp.plotvars.plot``, country borders are added using normal 
-#   `Cartopy operations <https://scitools.org.uk/cartopy/docs/latest/reference/index.html>`_ 
+# - the subplots for plotting are selected using
+#   `cfplot.gpos <https://ajheaps.github.io/cf-plot/gpos.html>`_ after which
+#   `cfplot.mapset <https://ajheaps.github.io/cf-plot/mapset.html>`_ is used to
+#   set the map limits and resolution for the subplots;
+# - and as cf-plot stores the plot in a plot object with the name
+#   ``cfp.plotvars.plot``, country borders are added using normal
+#   `Cartopy operations <https://scitools.org.uk/cartopy/docs/latest/reference/index.html>`_
 #   on the ``cfp.plotvars.mymap`` object:
 import cartopy.feature as cfeature
 

docs/_downloads/plot_13_recipe.ipynb

@@ -148,7 +148,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "8. The line for variable ``nino34_anomaly`` calculates the standardized\nanomaly for each time step in the ``nino34_index`` data. It subtracts the\n``climatology`` from the ``nino34_index`` and then divides by the ``std_dev``.\nThe resulting ``nino34_anomaly`` data represents how much the SST in the Ni\u00f1o \n3.4 region deviates from the 1961-1990 average, in units of standard \ndeviations. This is a common way to quantify climate anomalies like El Ni\u00f1o \nand La Ni\u00f1a events:\n\n"
+        "8. The line for variable ``nino34_anomaly`` calculates the standardized\nanomaly for each time step in the ``nino34_index`` data. It subtracts the\n``climatology`` from the ``nino34_index`` and then divides by the ``std_dev``.\nThe resulting ``nino34_anomaly`` data represents how much the SST in the Ni\u00f1o\n3.4 region deviates from the 1961-1990 average, in units of standard\ndeviations. This is a common way to quantify climate anomalies like El Ni\u00f1o\nand La Ni\u00f1a events:\n\n"
       ]
     },
     {
@@ -195,7 +195,7 @@
       },
       "outputs": [],
       "source": [
-        "elnino = nino34_rolling >= 0.4\nlanina = nino34_rolling <= -0.4\n\ncfp.gset(xmin='1940-1-1', xmax='2022-12-31', ymin=-3, ymax=3)\n\ncfp.gopen(figsize=(10, 6))\ncfp.lineplot(\n    nino34_rolling,\n    color=\"black\",\n    title=\"SST Anomaly in Ni\u00f1o 3.4 Region (5N-5S, 120-170W)\",\n    ylabel=\"Temperature anomaly ($\\degree C$)\",\n    xlabel=\"Year\",\n)\ncfp.plotvars.plot.axhline(\n    0.4, color=\"red\", linestyle=\"--\", label=\"El Ni\u00f1o Threshold\"\n)\ncfp.plotvars.plot.axhline(\n    -0.4, color=\"blue\", linestyle=\"--\", label=\"La Ni\u00f1a Threshold\"\n)\ncfp.plotvars.plot.axhline(0, color=\"black\", linestyle=\"-\", linewidth=1)\ncfp.plotvars.plot.fill_between(\n    nino34_rolling.coordinate(\"T\").array,\n    0.4,\n    nino34_rolling.array.squeeze(),\n    where=elnino.squeeze(),\n    color=\"red\",\n    alpha=0.3,\n)\ncfp.plotvars.plot.fill_between(\n    nino34_rolling.coordinate(\"T\").array,\n    -0.4,\n    nino34_rolling.array.squeeze(),\n    where=lanina.squeeze(),\n    color=\"blue\",\n    alpha=0.3,\n)\ncfp.plotvars.plot.legend(frameon=False, loc=\"lower center\", ncol=2)\ncfp.gclose()"
+        "elnino = nino34_rolling >= 0.4\nlanina = nino34_rolling <= -0.4\n\ncfp.gset(xmin=\"1940-1-1\", xmax=\"2022-12-31\", ymin=-3, ymax=3)\n\ncfp.gopen(figsize=(10, 6))\ncfp.lineplot(\n    nino34_rolling,\n    color=\"black\",\n    title=\"SST Anomaly in Ni\u00f1o 3.4 Region (5N-5S, 120-170W)\",\n    ylabel=\"Temperature anomaly ($\\degree C$)\",\n    xlabel=\"Year\",\n)\ncfp.plotvars.plot.axhline(\n    0.4, color=\"red\", linestyle=\"--\", label=\"El Ni\u00f1o Threshold\"\n)\ncfp.plotvars.plot.axhline(\n    -0.4, color=\"blue\", linestyle=\"--\", label=\"La Ni\u00f1a Threshold\"\n)\ncfp.plotvars.plot.axhline(0, color=\"black\", linestyle=\"-\", linewidth=1)\ncfp.plotvars.plot.fill_between(\n    nino34_rolling.coordinate(\"T\").array,\n    0.4,\n    nino34_rolling.array.squeeze(),\n    where=elnino.squeeze(),\n    color=\"red\",\n    alpha=0.3,\n)\ncfp.plotvars.plot.fill_between(\n    nino34_rolling.coordinate(\"T\").array,\n    -0.4,\n    nino34_rolling.array.squeeze(),\n    where=lanina.squeeze(),\n    color=\"blue\",\n    alpha=0.3,\n)\ncfp.plotvars.plot.legend(frameon=False, loc=\"lower center\", ncol=2)\ncfp.gclose()"
       ]
     }
   ],
@@ -215,7 +215,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,

docs/_downloads/plot_13_recipe.py

@@ -182,9 +182,9 @@
 # 8. The line for variable ``nino34_anomaly`` calculates the standardized
 # anomaly for each time step in the ``nino34_index`` data. It subtracts the
 # ``climatology`` from the ``nino34_index`` and then divides by the ``std_dev``.
-# The resulting ``nino34_anomaly`` data represents how much the SST in the Niño 
-# 3.4 region deviates from the 1961-1990 average, in units of standard 
-# deviations. This is a common way to quantify climate anomalies like El Niño 
+# The resulting ``nino34_anomaly`` data represents how much the SST in the Niño
+# 3.4 region deviates from the 1961-1990 average, in units of standard
+# deviations. This is a common way to quantify climate anomalies like El Niño
 # and La Niña events:
 nino34_anomaly = (nino34_index - climatology) / std_dev
 
@@ -228,7 +228,7 @@
 elnino = nino34_rolling >= 0.4
 lanina = nino34_rolling <= -0.4
 
-cfp.gset(xmin='1940-1-1', xmax='2022-12-31', ymin=-3, ymax=3)
+cfp.gset(xmin="1940-1-1", xmax="2022-12-31", ymin=-3, ymax=3)
 
 cfp.gopen(figsize=(10, 6))
 cfp.lineplot(

docs/_downloads/plot_14_recipe.ipynb

@@ -233,7 +233,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.9"
+      "version": "3.10.8"
     }
   },
   "nbformat": 4,