Merge pull request #200 from GeoscienceAustralia/bren/fix-req-list

Fix requirements listings

.travis.yml

@@ -27,6 +27,8 @@ before_install:
   - pip install Cython --install-option="--no-cython-compile"
   - pip install pytest-cov
   - pip install coveralls
+  - pip install pip-tools
+  - pip-compile --upgrade
 
 install:
   - pip install -r requirements.txt

requirements.in

@@ -0,0 +1,40 @@
+cartopy
+chardet==3.0.4
+Click>=6.0
+Cython>=0.22.1 # `module load` on NCI
+deprecated
+descartes
+geographiclib
+h5py>=2.6.0
+joblib
+lxml>=3.3.5
+matplotlib>=1.4.3,<=3.2.2  # nci version with python=3.4, 3.2.2+ not compatbile with basemap
+mpi4py==3.0.0
+netCDF4>=1.3.0
+numexpr
+numpy>=1.9.2
+obspy>=1.1.0  # 1.0.3 does not have sc3ml read functionality
+obspyh5
+ordered-set
+pandas
+psutil
+pyasdf
+pyepsg>=0.4.0
+pykml
+pyproj
+pyqtgraph
+pytables==3.5.2; sys_platform=='win32'
+PyWavelets
+pyyaml
+PyYAML>=3.11
+requests
+rf==0.8.0
+scikit-learn
+scipy>=0.15.1
+shapely --no-binary=shapely
+sortedcontainers
+tables==3.5.2; sys_platform!='win32'
+tqdm
+ujson
+urllib3
+xlrd

requirements.txt

@@ -1,34 +1,72 @@
-sphinx>=1.8
-ordered-set
-numpy>=1.16.4
-pandas
-pyproj
-h5py
-pyasdf
-obspy>=1.2.0
-obspyh5
-shapely --no-binary=shapely
-geographiclib
-cartopy>=0.18.0
-pytables==3.5.2; sys_platform=="win32"
-tables==3.5.2; sys_platform!="win32"
-mpi4py
-psutil
-#geopandas
-pytest>=4.6.5
-joblib
-click
-netCDF4==1.5.2
-ujson
-deprecated
-pyyaml
-requests
-Cython  # On NCI, use module load
-tqdm
-rf==0.8.0
-sortedcontainers
-scikit-learn
-urllib3
-pykml
-PyWavelets
-descartes
+#
+# This file is autogenerated by pip-compile
+# To update, run:
+#
+#    pip-compile
+#
+--no-binary shapely
+
+cartopy==0.18.0           # via -r requirements.in, rf
+certifi==2020.6.20        # via requests
+cftime==1.2.1             # via netcdf4
+chardet==3.0.4            # via -r requirements.in, requests
+click==7.1.2              # via -r requirements.in
+colorama==0.4.3           # via pyasdf
+cycler==0.10.0            # via matplotlib
+cython==0.29.21           # via -r requirements.in
+decorator==4.4.2          # via networkx, obspy, rf
+deprecated==1.2.10        # via -r requirements.in
+descartes==1.1.0          # via -r requirements.in
+dill==0.3.2               # via pyasdf
+future==0.18.2            # via obspy
+geographiclib==1.50       # via -r requirements.in, rf
+h5py==2.10.0              # via -r requirements.in, obspyh5, pyasdf
+idna==2.10                # via requests
+isodate==0.6.0            # via rdflib
+joblib==0.16.0            # via -r requirements.in, scikit-learn
+kiwisolver==1.2.0         # via matplotlib
+lxml==4.5.2               # via -r requirements.in, obspy, prov, pykml
+matplotlib==3.2.2         # via -r requirements.in, descartes, obspy, rf
+mock==4.0.2               # via tables
+mpi4py==3.0.0             # via -r requirements.in
+netcdf4==1.5.4            # via -r requirements.in
+networkx==2.4             # via prov
+numexpr==2.7.1            # via -r requirements.in, tables
+numpy==1.19.1             # via -r requirements.in, cartopy, cftime, h5py, matplotlib, netcdf4, numexpr, obspy, obspyh5, pandas, pyasdf, pyqtgraph, pywavelets, rf, scikit-learn, scipy, tables
+obspy==1.2.2              # via -r requirements.in, obspyh5, pyasdf, rf
+obspyh5==0.5.0            # via -r requirements.in
+ordered-set==4.0.2        # via -r requirements.in
+pandas==1.1.0             # via -r requirements.in
+prov==1.5.3               # via pyasdf
+psutil==5.7.2             # via -r requirements.in
+pyasdf==0.7.3             # via -r requirements.in
+pyepsg==0.4.0             # via -r requirements.in
+pykml==0.2.0              # via -r requirements.in
+pyparsing==2.4.7          # via matplotlib, rdflib
+pyproj==2.6.1.post1       # via -r requirements.in
+pyqtgraph==0.11.0         # via -r requirements.in
+pyshp==2.1.0              # via cartopy
+python-dateutil==2.8.1    # via matplotlib, pandas, prov
+pytz==2020.1              # via pandas
+pywavelets==1.1.1         # via -r requirements.in
+pyyaml==5.3.1             # via -r requirements.in
+rdflib==5.0.0             # via prov
+requests==2.24.0          # via -r requirements.in, obspy, pyepsg
+rf==0.8.0                 # via -r requirements.in
+scikit-learn==0.23.1      # via -r requirements.in
+scipy==1.5.2              # via -r requirements.in, obspy, rf, scikit-learn
+shapely==1.7.0            # via -r requirements.in, cartopy, rf
+six==1.15.0               # via cartopy, cycler, h5py, prov, python-dateutil, rdflib, tables
+sortedcontainers==2.2.2   # via -r requirements.in
+sqlalchemy==1.3.18        # via obspy
+tables==3.5.2 ; sys_platform != "win32"  # via -r requirements.in
+threadpoolctl==2.1.0      # via scikit-learn
+toeplitz==0.3.1           # via rf
+tqdm==4.48.1              # via -r requirements.in, rf
+ujson==3.1.0              # via -r requirements.in
+urllib3==1.25.10          # via -r requirements.in, requests
+wrapt==1.12.1             # via deprecated
+xlrd==1.2.0               # via -r requirements.in
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools

setup.py

@@ -5,6 +5,13 @@
 python_version = sys.version_info
 __version__ = "1.0.0"  # FZ-2020-07-02 tag this as version 1.0.0 after EFTF-1 completed and EFTF-X began.
 
+# Read dependencies from requirements.in
+with open('requirements.in', 'r') as f:
+    install_reqs = f.readlines()
+    # Remove comments and pip options (e.g. '--no-binary')
+    install_reqs = [s.strip().split('#')[0].split('--')[0] for s in install_reqs]
+
+print(install_reqs)
 
 class PyTest(TestCommand, object):
     user_options = [('pytest-args=', 'a', "Arguments to pass to pytest")]
@@ -80,47 +87,28 @@ def run_tests(self):
     # numpy preinstall required due to obspy
     # mpi4py  preinstall required due to h5py
     setup_requires=[
-        'numpy >= 1.9.2',
+        'numpy',
         'mpi4py==3.0.0',
         'decorator>=4.1.0',
         'setuptools>=36.2.1'
     ],
-    install_requires=[
-        'Click >= 6.0',
-        'numpy >= 1.9.2',
-        'Cython >= 0.22.1',
-        'mpi4py == 3.0.0',
-        'scipy >= 0.15.1',
-        'PyYAML >= 3.11',
-        'matplotlib >= 1.4.3',  # nci version with python=3.4
-        'joblib',
-        'obspy >= 1.1.0',  # 1.0.3 does not have sc3ml read functionality
-        'h5py >= 2.6.0',
-        'pyasdf',
-        'pyqtgraph',
-        'pandas',
-        # 'phasepapy == 1.1.1',
-        # 'basemap == 1.1.0',
-        'netCDF4 >= 1.3.0',
-        'chardet == 3.0.4',
-        'lxml >= 3.3.5'
-    ],
+    install_requires=install_reqs,
     extras_require={
         'dev': [
             'sphinx',
             'ghp-import',
             'sphinxcontrib-programoutput',
             'pytest-cov',
-            'coverage == 4.4.1',
-            'codecov == 2.0.9',
+            'coverage==4.4.1',
+            'codecov==2.0.9',
             'tox',
-            'pytest >= 3.1.0',
-            'pytest-lazy-fixture >= 0.4.0',
-            'pytest-flake8 >= 0.8.1',
-            'pytest-mock >= 1.6.0',
-            'pytest-cov == 2.5.1',
-            'pytest-regtest >= 0.15.1',
-            'flake8-docstrings >= 1.1.0',
+            'pytest>=3.1.0',
+            'pytest-lazy-fixture>=0.4.0',
+            'pytest-flake8>=0.8.1',
+            'pytest-mock>=1.6.0',
+            'pytest-cov==2.5.1',
+            'pytest-regtest>=0.15.1',
+            'flake8-docstrings>=1.1.0',
         ]
     },
     license="GNU GENERAL PUBLIC LICENSE v3",