Replace tables/pytables with h5py (#1299)

kandersolar · web-flow · commit 403f65e42900 · 2021-08-30T09:35:17.000-07:00
* Revert "Make tables a required dependency (#1287)" This reverts commit 65782fd. * replace tables with h5py * fix pr number * fiddle with 3.6-min yml * fix clearsky.rst * fiddle with whatsnew
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -12,7 +12,7 @@ jobs:
     vmImage: ubuntu-16.04
 
 
-- template: ci/azure/posix_no_39.yml
+- template: ci/azure/posix.yml
   parameters:
     name: Test_bare_macOS
     vmImage: macOS-10.14
diff --git a/benchmarks/asv.conf.json b/benchmarks/asv.conf.json
@@ -119,7 +119,7 @@
             "pandas": "0.22.0",
             "scipy": "1.2.0",
             // Note: these don't have a minimum in setup.py
-            "pytables": "3.6.1",
+            "h5py": "2.10.0",
             "ephem": "3.7.6.0",
             "numba": "0.36.1",
         },
@@ -129,7 +129,7 @@
             "numpy": "",
             "pandas": "",
             "scipy": "",
-            "pytables": "",
+            "h5py": "",
             "ephem": "",
             "numba": ""
         },
diff --git a/ci/azure/posix_no_39.yml b/ci/azure/posix_no_39.yml
diff --git a/ci/requirements-py36-min.yml b/ci/requirements-py36-min.yml
@@ -5,7 +5,6 @@ dependencies:
     - coveralls
     - nose
     - pip
-    - pytables  # tables when using pip+PyPI
     - pytest
     - pytest-cov
     - pytest-mock
@@ -15,10 +14,10 @@ dependencies:
     - requests
     - pip:
         - dataclasses
+        - h5py==3.1.0
         - numpy==1.12.0
         - pandas==0.22.0
         - scipy==1.2.0
         - pytest-rerunfailures # conda version is >3.6
         - pytest-remotedata # conda package is 0.3.0, needs > 0.3.1
         - requests-mock
-        - numexpr==2.6.2 # needed for tables, but newest version is not compatible with numpy 1.12
diff --git a/ci/requirements-py36.yml b/ci/requirements-py36.yml
@@ -3,17 +3,16 @@ channels:
     - defaults
     - conda-forge
 dependencies:
-    - blosc=1.14.3  # newest version breaks tables (pytables) on windows
     - coveralls
     - cython
     - ephem
+    - h5py
     - netcdf4
     - nose
     - numba
     - numpy >= 1.12.0
     - pandas >= 0.22.0
     - pip
-    - pytables  # tables when using pip+PyPI
     - pytest
     - pytest-cov
     - pytest-mock
diff --git a/ci/requirements-py37.yml b/ci/requirements-py37.yml
@@ -3,17 +3,16 @@ channels:
     - defaults
     - conda-forge
 dependencies:
-    - blosc=1.14.3  # newest version breaks tables (pytables) on windows
     - coveralls
     - cython
     - ephem
+    - h5py
     - netcdf4
     - nose
     - numba
     - numpy >= 1.12.0
     - pandas >= 0.22.0
     - pip
-    - pytables  # tables when using pip+PyPI
     - pytest
     - pytest-cov
     - pytest-mock
diff --git a/ci/requirements-py38.yml b/ci/requirements-py38.yml
@@ -6,13 +6,13 @@ dependencies:
     - coveralls
     - cython
     - ephem
+    - h5py
     - netcdf4
     - nose
     - numba
     - numpy >= 1.12.0
     - pandas >= 0.22.0
     - pip
-    - pytables  # tables when using pip+PyPI
     - pytest
     - pytest-cov
     - pytest-mock
diff --git a/ci/requirements-py39.yml b/ci/requirements-py39.yml
@@ -6,13 +6,13 @@ dependencies:
     - coveralls
     - cython
     - ephem
+    - h5py
     # - netcdf4  # pulls in a different version of numpy with ImportError
     - nose
     # - numba  # python 3.9 compat in early 2021
     - numpy >= 1.12.0
     - pandas >= 0.22.0
     - pip
-    - pytables  # tables when using pip+PyPI
     - pytest
     - pytest-cov
     - pytest-mock
diff --git a/docs/sphinx/source/clearsky.rst b/docs/sphinx/source/clearsky.rst
@@ -132,16 +132,16 @@ the year. You could run it in a loop to create plots for all months.
 
     In [1]: import os
 
-    In [1]: import tables
+    In [1]: import h5py
 
     In [1]: pvlib_path = os.path.dirname(os.path.abspath(pvlib.clearsky.__file__))
 
     In [1]: filepath = os.path.join(pvlib_path, 'data', 'LinkeTurbidities.h5')
 
     In [1]: def plot_turbidity_map(month, vmin=1, vmax=100):
        ...:     plt.figure();
-       ...:     with tables.open_file(filepath) as lt_h5_file:
-       ...:         ltdata = lt_h5_file.root.LinkeTurbidity[:, :, month-1]
+       ...:     with h5py.File(filepath, 'r') as lt_h5_file:
+       ...:         ltdata = lt_h5_file['LinkeTurbidity'][:, :, month-1]
        ...:     plt.imshow(ltdata, vmin=vmin, vmax=vmax);
        ...:     # data is in units of 20 x turbidity
        ...:     plt.title('Linke turbidity x 20, ' + calendar.month_name[month]);
diff --git a/docs/sphinx/source/installation.rst b/docs/sphinx/source/installation.rst
@@ -235,7 +235,6 @@ A handful of pvlib-python features require additional packages that must
 be installed separately using pip or conda. These packages/features
 include:
 
-* pytables (tables on PyPI): Linke turbidity look up for clear sky models
 * statsmodels: parameter fitting
 * numba: fastest solar position calculations
 * pyephem: solar positions calculations using an astronomical library
diff --git a/docs/sphinx/source/whatsnew/v0.9.0.rst b/docs/sphinx/source/whatsnew/v0.9.0.rst
@@ -233,7 +233,8 @@ Documentation
 Requirements
 ~~~~~~~~~~~~
 * ``dataclasses`` is required for python 3.6 (:pull:`1076`)
-* ``tables`` is now required instead of optional (:issue:`1286`, :pull:`1287`)
+* ``h5py`` is now a required dependency.  This replaces ``tables``, which was formerly
+  an optional dependency.  (:pull:`1299`, :issue:`1252`, :issue:`1286`)
 
 Contributors
 ~~~~~~~~~~~~
diff --git a/pvlib/clearsky.py b/pvlib/clearsky.py
@@ -11,7 +11,7 @@
 import pandas as pd
 from scipy.optimize import minimize_scalar
 from scipy.linalg import hankel
-import tables
+import h5py
 
 from pvlib import atmosphere, tools
 
@@ -194,9 +194,8 @@ def lookup_linke_turbidity(time, latitude, longitude, filepath=None,
     latitude_index = _degrees_to_index(latitude, coordinate='latitude')
     longitude_index = _degrees_to_index(longitude, coordinate='longitude')
 
-    with tables.open_file(filepath) as lt_h5_file:
-        lts = lt_h5_file.root.LinkeTurbidity[latitude_index,
-                                             longitude_index, :]
+    with h5py.File(filepath, 'r') as lt_h5_file:
+        lts = lt_h5_file['LinkeTurbidity'][latitude_index, longitude_index]
 
     if interp_turbidity:
         linke_turbidity = _interpolate_turbidity(lts, time)
diff --git a/setup.py b/setup.py
@@ -43,7 +43,7 @@
                     'pytz',
                     'requests',
                     'scipy >= 1.2.0',
-                    'tables']
+                    'h5py']
 
 # include dataclasses as a dependency only on python 3.6
 if sys.version_info.major == 3 and sys.version_info.minor == 6:
@@ -58,7 +58,7 @@
                  'cftime >= 1.1.1'],
     'doc': ['ipython', 'matplotlib', 'sphinx == 3.1.2',
             'sphinx_rtd_theme==0.5.0', 'sphinx-gallery', 'docutils == 0.15.2',
-            'pillow', 'netcdf4', 'siphon', 'tables',
+            'pillow', 'netcdf4', 'siphon',
             'sphinx-toggleprompt >= 0.0.5'],
     'test': TESTS_REQUIRE
 }
