Bump minimum numpy version to 1.20 (#6834)

Co-authored-by: Deepak Cherian <[email protected]>
Co-authored-by: dcherian <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

ci/requirements/all-but-dask.yml

@@ -18,7 +18,7 @@ dependencies:
   - h5py
   - hdf5
   - hypothesis
-  - lxml # Optional dep of pydap
+  - lxml  # Optional dep of pydap
   - matplotlib-base
   - nc-time-axis
   - netcdf4
@@ -30,7 +30,7 @@ dependencies:
   - pip
   - pseudonetcdf
   - pydap
-  # - pynio: not compatible with netCDF4>1.5.3; only tested in py37-bare-minimum
+  # - pynio  # not compatible with netCDF4>1.5.3, see #4491
   - pytest
   - pytest-cov
   - pytest-env

ci/requirements/bare-minimum.yml

@@ -10,6 +10,6 @@ dependencies:
   - pytest-cov
   - pytest-env
   - pytest-xdist
-  - numpy=1.19
-  - packaging=20.0
-  - pandas=1.2
+  - numpy=1.20
+  - packaging=21.0
+  - pandas=1.3

ci/requirements/doc.yml

@@ -18,9 +18,9 @@ dependencies:
   - nbsphinx
   - netcdf4>=1.5
   - numba
-  - numpy>=1.17
-  - packaging>=20.0
-  - pandas>=1.0
+  - numpy>=1.20
+  - packaging>=21.0
+  - pandas>=1.3
   - pooch
   - pip
   - pydata-sphinx-theme>=0.4.3

ci/requirements/environment-windows.yml

@@ -17,7 +17,7 @@ dependencies:
   - hdf5
   - hypothesis
   - iris
-  - lxml # Optional dep of pydap
+  - lxml  # Optional dep of pydap
   - matplotlib-base
   - nc-time-axis
   - netcdf4

ci/requirements/environment.yml

@@ -19,7 +19,7 @@ dependencies:
   - hdf5
   - hypothesis
   - iris
-  - lxml # Optional dep of pydap
+  - lxml  # Optional dep of pydap
   - matplotlib-base
   - nc-time-axis
   - netcdf4
@@ -34,7 +34,7 @@ dependencies:
   - pre-commit
   - pseudonetcdf
   - pydap
-  # - pynio: not compatible with netCDF4>1.5.3; only tested in py37-bare-minimum
+  # - pynio  # not compatible with netCDF4>1.5.3, see #4491
   - pytest
   - pytest-cov
   - pytest-env

ci/requirements/min-all-deps.yml

@@ -8,33 +8,35 @@ dependencies:
   # When upgrading python, numpy, or pandas, must also change
   # doc/installing.rst and setup.py.
   - python=3.8
-  - boto3=1.13
+  - boto3=1.18
   - bottleneck=1.3
   - cartopy=0.19
   - cdms2=3.1
   - cfgrib=0.9
-  - cftime=1.4
+  - cftime=1.5
   - coveralls
-  - dask-core=2021.08.0
-  - distributed=2021.08.0
+  - dask-core=2021.09
+  - distributed=2021.09
   - flox=0.5
   - h5netcdf=0.11
+  # h5py and hdf5 tend to cause conflicrs
+  # for e.g. hdf5 1.12 conflicts with h5py=3.1
+  # prioritize bumping other packages instead
   - h5py=3.1
-  # hdf5 1.12 conflicts with h5py=3.1
   - hdf5=1.10
   - hypothesis
-  - iris=2.4
+  - iris=3.1
   - lxml=4.6  # Optional dep of pydap
   - matplotlib-base=3.4
-  - nc-time-axis=1.2
+  - nc-time-axis=1.3
   # netcdf follows a 1.major.minor[.patch] convention
   # (see https://github.com/Unidata/netcdf4-python/issues/1090)
   # bumping the netCDF4 version is currently blocked by #4491
   - netcdf4=1.5.3
-  - numba=0.53
-  - numpy=1.19
-  - packaging=20.0
-  - pandas=1.2
+  - numba=0.54
+  - numpy=1.20
+  - packaging=21.0
+  - pandas=1.3
   - pint=0.17
   - pip
   - pseudonetcdf=3.1
@@ -45,11 +47,11 @@ dependencies:
   - pytest-env
   - pytest-xdist
   - rasterio=1.2
-  - scipy=1.6
+  - scipy=1.7
   - seaborn=0.11
-  - sparse=0.12
+  - sparse=0.13
   - toolz=0.11
-  - typing_extensions=3.7
-  - zarr=2.8
+  - typing_extensions=3.10
+  - zarr=2.10
   - pip:
     - numbagg==0.1

doc/getting-started-guide/installing.rst

@@ -7,9 +7,9 @@ Required dependencies
 ---------------------
 
 - Python (3.8 or later)
-- `numpy <https://www.numpy.org/>`__ (1.19 or later)
-- `packaging <https://packaging.pypa.io/en/latest/#>`__ (20.0 or later)
-- `pandas <https://pandas.pydata.org/>`__ (1.2 or later)
+- `numpy <https://www.numpy.org/>`__ (1.20 or later)
+- `packaging <https://packaging.pypa.io/en/latest/#>`__ (21.0 or later)
+- `pandas <https://pandas.pydata.org/>`__ (1.3 or later)
 
 .. _optional-dependencies:
 

doc/whats-new.rst

@@ -32,6 +32,26 @@ New Features
 Breaking changes
 ~~~~~~~~~~~~~~~~
 
+- The minimum versions of some dependencies were changed:
+
+  ========================== =========  ========
+   Package                         Old      New
+  ========================== =========  ========
+   cftime                          1.4      1.5
+   distributed                 2021.08  2021.09
+   dask                        2021.08  2021.09
+   iris                            2.4      3.1
+   nc-time-axis                    1.2      1.3
+   numba                          0.53     0.54
+   numpy                          1.19     1.20
+   pandas                          1.2      1.3
+   packaging                      20.0     21.0
+   scipy                           1.6      1.7
+   sparse                         0.12     0.13
+   typing_extensions               3.7     3.10
+   zarr                            2.8     2.10
+  ========================== =========  ========
+
 
 Deprecations
 ~~~~~~~~~~~~

requirements.txt

@@ -2,6 +2,6 @@
 # it exists to let GitHub build the repository dependency graph
 # https://help.github.com/en/github/visualizing-repository-data-with-graphs/listing-the-packages-that-a-repository-depends-on
 
-numpy >= 1.18
-packaging >= 20.0
-pandas >= 1.1
+numpy >= 1.20
+packaging >= 21.0
+pandas >= 1.3

setup.cfg

@@ -75,9 +75,9 @@ zip_safe = False  # https://mypy.readthedocs.io/en/latest/installed_packages.htm
 include_package_data = True
 python_requires = >=3.8
 install_requires =
-    numpy >= 1.19  # recommended to use >= 1.22 for full quantile method support
-    pandas >= 1.2
-    packaging >= 20.0
+    numpy >= 1.20  # recommended to use >= 1.22 for full quantile method support
+    pandas >= 1.3
+    packaging >= 21.0
 
 [options.extras_require]
 io =