bump python to version 3.8 in conda env config files and mdtf_test ya…

…ml (#415)

* bump python to version 3.8 in conda env config files and mdtf_test yaml
fix typo in conda_init.sh
bump other package versions in yamls to be consistent with base env

* update python 3.7 to python 3.8 in docs, requirements, and version checking

* replace call to (apparently) deprecated xarray.ufuncs.isnan with np.isnan in mixed_layer_depth.py

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,7 +14,7 @@ operating system(s) you ran your tests on.
 **Checklist:**
 - [ ] I have reviewed my own code to ensure that if follows the [POD development guidelines](https://mdtf-diagnostics.readthedocs.io/en/latest/sphinx/dev_guidelines.html)
 - [ ] My branch is up-to-date with the NOAA-GFDL main branch, and all merge conflicts are resolved
-- [ ] The scripts are written in Python 3.7 or above (preferred; required if funded by a CPO grant), NCL, or R
+- [ ] The scripts are written in Python 3.8 or above (preferred; required if funded by a CPO grant), NCL, or R
 - [ ] All of my scripts are in the diagnostics/[POD short name] subdirectory, and include a main_driver script, template html, and settings.jsonc file
 - [ ] I have made corresponding changes to the documentation in the POD's doc/ subdirectory
 - [ ] I have requested that the framework developers add packages required by my POD to the python3, NCL, or R environment yaml file if necessary, and my environment builds with `conda_env_setup.sh` 

.github/workflows/mdtf_tests.yml

@@ -61,7 +61,7 @@ jobs:
       uses: conda-incubator/setup-miniconda@v2
       with:
         miniconda-version: "latest"
-        python-version: 3.7
+        python-version: 3.8
         mamba-version: "*"
         channels: conda-forge,defaults
     - name: Verify miniconda

.readthedocs.yml

@@ -20,7 +20,7 @@ formats:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: doc/requirements.txt
     - method: pip

diagnostics/mixed_layer_depth/mixed_layer_depth.py

@@ -226,7 +226,7 @@ def computemld(fieldso, fieldthetao):
     )  # units 'meters'
 
     # set MLD to water depth where MLD is NaN
-    mld = mld.where(~xr.ufuncs.isnan(mld), bottom_depth)
+    mld = mld.where(~np.isnan(mld), bottom_depth)
 
     return mld
 

doc/conf.py

@@ -474,7 +474,7 @@ def patched_parse(self):
 # -- Options for intersphinx extension -----------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html
 intersphinx_mapping = {
-    'python': ('https://docs.python.org/3.7', None),
+    'python': ('https://docs.python.org/3.8', None),
     'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
     'numpy': ('https://docs.scipy.org/doc/numpy/', None),
     'xarray': ('https://xarray.pydata.org/en/stable/', None)

doc/sphinx/dev_guidelines.rst

@@ -10,11 +10,11 @@ The framework itself is written in Python, and can call PODs written in any scri
 
 - To achieve portability, the MDTF **cannot** accept PODs written in closed-source languages (e.g., MATLAB and IDL; try `Octave <https://www.gnu.org/software/octave/>`__ and `GDL <https://github.com/gnudatalanguage/gdl>`__ if possible). We also **cannot** accept PODs written in compiled languages (e.g., C or Fortran): installation would rapidly become impractical if users had to check compilation options for each POD.
 
-- Python is strongly encouraged for new PODs; PODs funded through the CPO grant are requested to be developed in Python. Python version >= 3.7 is required. Official support for Python 2 was discontinued as of January 2020.
+- Python is strongly encouraged for new PODs; PODs funded through the CPO grant are requested to be developed in Python. Python version >= 3.8 is required. Official support for Python 2 was discontinued as of January 2020.
 
 - If your POD was previously developed in NCL or R (and development is *not* funded through a CPO grant), you do not need to re-write existing scripts in Python 3 if doing so is likely to introduce new bugs into stable code, especially if you’re unfamiliar with Python.
 
-- If scripts were written in closed-source languages, translation to Python 3.7 or above is required.
+- If scripts were written in closed-source languages, translation to Python 3.8 or above is required.
 
 Preparation for POD implementation
 ----------------------------------

doc/sphinx/dev_start.rst

@@ -32,7 +32,7 @@ Installing dependencies via conda
 Regardless of development language, we strongly recommend that developers use conda to manage their language and library versions. Note that Conda is not Python-specific, but allows coexisting versioned environments of most scripting languages, including, `R <https://anaconda.org/conda-forge/r-base>`__, `NCL <https://anaconda.org/conda-forge/ncl>`__, `Ruby <https://anaconda.org/conda-forge/ruby>`__, `PyFerret <https://anaconda.org/conda-forge/pyferret>`__, and more.
 
 
-Python-based PODs should be written in Python 3.7 or newer. We provide a developer version of the python3_base environment (described below) that includes Jupyter and other developer-specific tools. This is not installed by default, and must be requested by passing the ``--all`` flag to the conda setup script:
+Python-based PODs should be written in Python 3.8 or newer. We provide a developer version of the python3_base environment (described below) that includes Jupyter and other developer-specific tools. This is not installed by default, and must be requested by passing the ``--all`` flag to the conda setup script:
 
 .. code-block:: console
 

mdtf_framework.py

@@ -9,8 +9,8 @@
 
 import sys
 # do version check before anything else
-if sys.version_info.major != 3 or sys.version_info.minor < 7:
-    sys.exit("ERROR: The MDTF package requires python >= 3.7. Please check "
+if sys.version_info.major != 3 or sys.version_info.minor < 8:
+    sys.exit("ERROR: The MDTF package requires python >= 3.8. Please check "
         "which version of python is on your $PATH (e.g. with `which python`.)\n"
         f"Attempted to run with following python version:\n{sys.version}")
 # passed; continue with imports

setup.py

@@ -26,7 +26,7 @@ def run(self):
 packages = find_packages()
 setup(
     name='MDTF-diagnostics',
-    version='3.0 beta 4',
+    version='3.0 beta 5',
     description='Process-oriented diagnostics for weather and climate simulations',
     license='LGPLv3',
     long_description=long_description,
@@ -38,13 +38,13 @@ def run(self):
             # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
             "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
             'Programming Language :: Python',
-            'Programming Language :: Python :: 3.7',
+            'Programming Language :: Python :: 3.8',
     ],
     scripts=[
         'mdtf_framework.py'
     ],
     packages=packages,
-    cmdclass={ # hook for post-install commands
+    cmdclass={  # hook for post-install commands
         'develop': PostDevelopCommand,
         'install': PostInstallCommand
     }

src/conda/_env_synthetic_data.yml

@@ -9,7 +9,7 @@ dependencies:
 - netCDF4=1.5.8
 - cftime=1.3.0
 - xarray>=2022.06.0
-- setuptools >= 49.1
+- setuptools>=49.1
 - esmf=8.2.0
 - esmpy=8.2.0
 - xesmf=0.6.2

src/conda/conda_init.sh

@@ -9,7 +9,7 @@
 # NOTE this has only been tested with conda 4.7.10 and later; I know earlier
 # versions had things in different places.
 
-# parse aruments manually
+# parse arguments manually
 _TEMP_CONDA_ROOT=""
 _TEMP_CONDA_EXE=""
 _v=1

src/conda/env_NCL_base.yml

@@ -3,7 +3,7 @@ channels:
 - conda-forge # NOTE: critical to give highest priority to conda-forge
 - defaults
 dependencies:
-- python=3.7
+- python=3.8
 # - ncl=6.5 # has a font rendering issue fixed in 6.6
 # - openblas=0.3.4 # otherwise ncl 6.5 installs but doesn't function on macs
 - ncl=6.6.2

src/conda/env_R_base.yml

@@ -3,7 +3,7 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- python=3.7
+- python=3.8
 - r-base
 - r-akima
 - r-colorramps

src/conda/env_base.yml

@@ -7,7 +7,7 @@ dependencies:
 # specify up to minor version number to provide a consistent environment for POD developers
 # versions are current as of Jul 2020
 # see https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/pkg-specs.html
-- python=3.7
+- python=3.8
 - ghostscript
 - numpy=1.19
 # - scipy=1.5.2

src/conda/env_convective_transition_diag.yml

@@ -3,15 +3,15 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- python=3.7
-- numpy=1.19
-- scipy=1.5.2
+- python=3.8
+- numpy=1.22.3
+- scipy=1.5.3
 - netCDF4=1.5.4
-- cftime=1.2
-- xarray=0.16
-- matplotlib=3.3
+- cftime=1.3.0
+- xarray>=0.20
+- matplotlib>=3.3
 - pandas<1.3
-- cartopy=0.18
-- numba = 0.51.2
-- networkx = 2.3
+- cartopy=0.20.0
+- numba=0.51.2
+- networkx=2.3
 - jupyterlab

src/conda/env_dev.yml

@@ -5,9 +5,9 @@ channels:
 - defaults
 dependencies:
 # contents of python3_base
-- python=3.7
+- python=3.8
 - numpy=1.19
-- scipy=1.5.2
+- scipy=1.5.3
 - netCDF4=1.5.4
 - cftime=1.2
 - xarray=0.16

src/conda/env_precip_buoy_diag.yml

@@ -3,12 +3,12 @@ channels:
 - conda-forge
 - defaults
 dependencies:
-- python=3.7
-- cython=0.29.21
-- xarray=0.16.2
-- numpy=1.18.5
+- python=3.8
+- cython>=0.29
+- xarray>=0.20
+- numpy=1.22.3
 - scipy=1.5.3
 - matplotlib=3.3.3
 - numba=0.52
-- pandas
-- dask
+- pandas<1.3
+- dask=2021.03.0

src/conda/env_python3_base.yml

@@ -7,9 +7,9 @@ dependencies:
 # versions are current as of Jul 2020
 # see https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/pkg-specs.
 
-- python=3.7
+- python=3.8
 - numpy=1.19
-- scipy=1.5.2
+- scipy=1.5.3
 - netCDF4=1.5.8
 - cftime>=1.6
 - xarray>=0.20
@@ -30,7 +30,7 @@ dependencies:
 - h5py=3.6.0
 - intake-xarray=0.6.0
 - nc-time-axis=1.4.1
-- pyyaml >=6.0
+- pyyaml>=6.0
 - pip=22.0.4
 - pip:
     - cmocean

src/install.py

@@ -5,8 +5,8 @@
 
 import sys
 # do version check before importing other stuff
-if sys.version_info[0] != 3 or sys.version_info[1] < 7:
-    sys.exit("ERROR: MDTF currently only supports python >= 3.7.*. Please check "
+if sys.version_info[0] != 3 or sys.version_info[1] < 8:
+    sys.exit("ERROR: MDTF currently only supports python >= 3.8.*. Please check "
     "which version is on your $PATH (e.g. with `which python`.)\n"
     f"Attempted to run with following python version:\n{sys.version}")
 # passed; continue with imports