Get CI working again (#925)

* Swap order of installs Something is borked with the mamba solver * Install dependencies explicitly `--no-deps` install of `fipy` is too fragile * Add newer opcodes * Ignore deprecated use of pkg_resources.declare_namespace * Catch errors from old Trilinos prerequisites * Update import of mmread * Log environment Hard to do regression testing when you don't know what was installed. Why is Azure so useless? * Replace deprecated `style` key in HTML template `style` superceded by `styles` in Sphinx 5.1 and removed in Sphinx 7 sphinx-doc/sphinx#11381
usnistgov · May 12, 2023 · a26aafd · a26aafd
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diff --git a/.azure/pipelines.yml b/.azure/pipelines.yml
@@ -34,7 +34,7 @@ stages:
       steps:
       - template: templates/install.yml
         parameters:
-          python_version: 3.10
+          python_version: 3
           conda_packages: 'hunspell'
 
       - bash: |
@@ -62,7 +62,7 @@ stages:
       steps:
       - template: templates/install.yml
         parameters:
-          python_version: 3.10
+          python_version: 3
           conda_packages: 'numpy'
 
       - bash: |
@@ -85,7 +85,7 @@ stages:
       steps:
       - template: templates/install.yml
         parameters:
-          python_version: 3.10
+          python_version: 3
           conda_packages: 'numpy'
 
       - bash: |
@@ -106,74 +106,74 @@ stages:
         matrix:
           linux-py3k-petsc:
             image: ubuntu-latest
-            python_version: 3.10
-            conda_packages: gmsh
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py petsc4py mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: petsc
             MPIRUN:
           linux-py3k-petsc-parallel:
             image: ubuntu-latest
-            python_version: 3.10
-            conda_packages: gmsh
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py petsc4py mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: petsc
             MPIRUN: 'mpirun -np 2'
           linux-py3k-scipy:
             image: ubuntu-latest
-            python_version: 3.10
-            conda_packages: gmsh
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: scipy
             MPIRUN:
-          linux-py37-trilinos:
+          linux-py3k-trilinos:
             image: ubuntu-latest
-            python_version: 3.7
-            conda_packages: 'gmsh pytrilinos'
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py pytrilinos mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: trilinos
             MPIRUN:
-          linux-py37-trilinos-parallel:
+          linux-py3k-trilinos-parallel:
             image: ubuntu-latest
-            python_version: 3.7
-            conda_packages: 'gmsh pytrilinos'
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py pytrilinos mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: trilinos
             MPIRUN: 'mpirun -np 2'
           macos-py27-pysparse:
             image: macos-latest
             python_version: 2.7
-            conda_packages: '"traitsui<7.0.0" "gmsh<4.0"'
+            conda_packages: 'numpy scipy matplotlib-base future packaging pysparse mayavi "traitsui<7.0.0" "gmsh<4.0"'
             FIPY_SOLVERS: pysparse
             MPIRUN:
           macos-py3k-petsc:
             image: macos-latest
-            python_version: 3.10
-            conda_packages: gmsh
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py petsc4py mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: petsc
             MPIRUN:
           macos-py3k-petsc-parallel:
             image: macos-latest
-            python_version: 3.10
-            conda_packages: gmsh
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py petsc4py mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: petsc
             MPIRUN: 'mpirun -np 2'
           macos-py3k-scipy:
             image: macos-latest
-            python_version: 3.10
-            conda_packages: gmsh
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: scipy
             MPIRUN:
-          macos-py37-trilinos:
+          macos-py3k-trilinos:
             image: macos-latest
-            python_version: 3.7
-            conda_packages: 'gmsh pytrilinos'
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py pytrilinos mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: trilinos
             MPIRUN:
-          macos-py37-trilinos-parallel:
+          macos-py3k-trilinos-parallel:
             image: macos-latest
-            python_version: 3.7
-            conda_packages: 'gmsh pytrilinos'
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py pytrilinos mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: trilinos
             MPIRUN: 'mpirun -np 2'
           windows-py3k-scipy:
             image: windows-latest
-            python_version: 3.10
-            conda_packages: gmsh
+            python_version: 3
+            conda_packages: 'numpy scipy matplotlib-base future packaging mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: scipy
             MPIRUN:
 
@@ -214,8 +214,8 @@ stages:
       steps:
       - template: templates/install.yml
         parameters:
-          python_version: 3.10
-          conda_packages: 'sphinx future matplotlib pandas imagemagick'
+          python_version: 3
+          conda_packages: 'numpy scipy matplotlib future packaging mpich mpi4py petsc4py mayavi "gmsh <4.0|>=4.5.2" sphinx pandas imagemagick'
 
       - bash: |
           source activate myEnvironment
@@ -233,6 +233,10 @@ stages:
           sudo apt-get --yes install texlive-extra-utils
         displayName: Install LaTeX
 
+      - bash: |
+          conda env export --name myEnvironment
+        displayName: Environment
+
       - bash: |
           source activate myEnvironment
           export ETS_TOOLKIT=null
@@ -260,13 +264,13 @@ stages:
           unix:
             image: ubuntu-latest
             python_version: 3.10
-            conda_packages: gmsh
+            conda_packages: 'numpy scipy matplotlib-base future packaging mpich mpi4py petsc4py mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: petsc
             MPIRUN:
           windows:
             image: windows-latest
             python_version: 3.10
-            conda_packages: gmsh
+            conda_packages: 'numpy scipy matplotlib-base future packaging mayavi "gmsh <4.0|>=4.5.2"'
             FIPY_SOLVERS: scipy
             MPIRUN:
 
@@ -291,6 +295,10 @@ stages:
         displayName: Build wheel
         condition: startsWith(variables.image, 'ubuntu')
 
+      - bash: |
+          conda env export --name myEnvironment
+        displayName: Environment
+
       - bash: |
           source activate myEnvironment
           python setup.py release --unix

diff --git a/.azure/templates/install.yml b/.azure/templates/install.yml
@@ -44,12 +44,10 @@ steps:
   - bash: |
       if [[ ${{ parameters.python_version }} == "2.7" ]]; then
         # mamba doesn't work in Py2.7; do mamba installs from base
-        mamba install --quiet --name myEnvironment --channel conda-forge --only-deps python=${{ parameters.python_version }} fipy
         mamba install --quiet --name myEnvironment --channel conda-forge python=${{ parameters.python_version }} ${{ parameters.conda_packages }}
       else
         # do mamba installs from environment on Py3k
         source activate myEnvironment
-        mamba install --quiet --channel conda-forge --only-deps python=${{ parameters.python_version }} fipy
         mamba install --quiet --channel conda-forge python=${{ parameters.python_version }} ${{ parameters.conda_packages }}
       fi
     displayName: Install Anaconda packages

diff --git a/INSTALLATION.rst b/INSTALLATION.rst
@@ -78,6 +78,17 @@ Recommended Method
      :term:`Gmsh` is an optional package because some versions are
      incompatible with :term:`FiPy`, so it must be requested explicitly.
 
+  .. note::
+
+     The `fipy conda-forge`_ package is a convenience. You may choose to
+     install packages explicitly, e.g.,::
+
+       $ conda create --name <MYFIPYENV> --channel conda-forge python=3 numpy scipy matplotlib-base future packaging mpich mpi4py petsc4py mayavi "gmsh <4.0|>=4.5.2"
+
+     or
+
+       $ conda create --name <MYFIPYENV> --channel conda-forge python=2.7 numpy scipy matplotlib-base future packaging pysparse mayavi "traitsui<7.0.0" "gmsh<4.0"
+
   .. attention::
 
      Windows x86_64 is fully supported, but this does not work on
@@ -150,7 +161,8 @@ Recommended Method
 .. _Windows: http://www.microsoft.com/windows/
 .. |CondaForge|    image:: https://anaconda.org/conda-forge/fipy/badges/installer/conda.svg
 .. _CondaForge:    https://anaconda.org/conda-forge/fipy
-.. _mamba: https://github.com/mamba-org/mamba
+.. _mamba: https://mamba.readthedocs.io/
+.. _fipy conda-forge: https://anaconda.org/conda-forge/fipy
 
 
 --------------

diff --git a/documentation/_themes/nist/basic_layout.html b/documentation/_themes/nist/basic_layout.html
@@ -94,7 +94,7 @@ <h3>{{ _('Navigation') }}</h3>
 {%- endmacro %}
 
 {%- macro css() %}
-    <link rel="stylesheet" href="{{ pathto('_static/' + style, 1) }}" type="text/css" />
+    <link rel="stylesheet" href="{{ pathto('_static/' + styles[-1], 1) }}" type="text/css" />
     <link rel="stylesheet" href="{{ pathto('_static/pygments.css', 1) }}" type="text/css" />
     {%- for css in css_files %}
       {%- if css|attr("filename") %}

diff --git a/fipy/matrices/trilinosMatrix.py b/fipy/matrices/trilinosMatrix.py
@@ -477,7 +477,10 @@ def exportMmf(self, filename):
     def numpyArray(self):
         import tempfile
         import os
-        from scipy.io import mmio
+        try:
+            from scipy.io import mmread
+        except ImportError:
+            from scipy.io.mmio import mmread
         from fipy.tools import parallelComm
 
         if parallelComm.procID == 0:
@@ -490,7 +493,7 @@ def numpyArray(self):
         self.exportMmf(mtxName)
 
         parallelComm.Barrier()
-        mtx = mmio.mmread(mtxName)
+        mtx = mmread(mtxName)
         parallelComm.Barrier()
 
         if parallelComm.procID == 0:

diff --git a/fipy/solvers/trilinos/__init__.py b/fipy/solvers/trilinos/__init__.py
@@ -34,15 +34,18 @@ def _dealWithTrilinosImportPathologies():
 
     from PyTrilinos import Epetra
 
-    import platform
-    if platform.dist()[0] == 'debian':
-        import PyTrilinos
-        if '10.0.4' in PyTrilinos.version():
-            # The package mpi4py is a required package if you are using
-            # Trilinos on a Debian platform with Trilinos version 10.0.4 due to
-            # a Trilinos bug (see <https://github.com/usnistgov/fipy/issues/301>).
-
-            from mpi4py import MPI
+    try:
+        import platform
+        if platform.dist()[0] == 'debian':
+            import PyTrilinos
+            if '10.0.4' in PyTrilinos.version():
+                # The package mpi4py is a required package if you are using
+                # Trilinos on a Debian platform with Trilinos version 10.0.4 due to
+                # a Trilinos bug (see <https://github.com/usnistgov/fipy/issues/301>).
+
+                from mpi4py import MPI
+    except:
+        pass
 
 _dealWithTrilinosImportPathologies()
 

diff --git a/fipy/tests/test.py b/fipy/tests/test.py
@@ -40,6 +40,13 @@ def runTests(self):
                                     message="`np\.int` is a deprecated alias for the builtin `int`.*",
                                     module="skfmm\.pfmm")
 
+            # Don't raise errors in scikits.umfpack
+            # due to deprecation of pkg_resources.declare_namespace
+            # raised in Python 3.7, but not newer
+            # (combination of PyTrilinos and Gmsh(?) forces this old configuration)
+            warnings.filterwarnings(action="default", category=DeprecationWarning,
+                                    message="Deprecated call to `pkg_resources\.declare_namespace\('scikits'\)`.*")
+
             super(DeprecationErroringTestProgram, self).runTests()
 
 class test(_test):