Merge branch 'master' into 0.4.X

.azure-ci/docker_scripts.sh

@@ -2,10 +2,11 @@
 
 set -x
 
-# Upgrade pip and setuptools. TODO: Monitor status of pip versions
+# Upgrade pip and setuptools, install wheel package
+# TODO: Monitor status of pip versions
 PYTHON_PATH=$(eval find "/opt/python/*${python_ver}*" -print)
 export PATH=${PYTHON_PATH}/bin:${PATH}
-pip install --upgrade pip==19.3.1 setuptools
+pip install --upgrade pip==20.2.4 setuptools
 
 # Install CMake
 pip install cmake
@@ -14,18 +15,17 @@ pip install cmake
 cd /io
 pip install -e ".[doc, tests]"
 
-# Test dev install with pytest and flake8
-pytest pyflagser --cov --cov-report xml
-flake8 --exit-zero /io/
+# Test dev install with pytest
+pytest pyflagser --no-cov --no-coverage-upload
 
 # Uninstal pyflagser dev
 pip uninstall -y pyflagser
 
 # Build wheels
-pip install wheel==0.34.1 auditwheel==3.1.0
 python setup.py bdist_wheel
 
 # Repair wheels with auditwheel
+pip install auditwheel
 auditwheel repair dist/*whl -w dist/
 # remove wheels that are not manylinux2010
 rm -rf dist/*-linux*.whl

RELEASE.rst

@@ -1,12 +1,47 @@
+Release 0.4.2
+=============
+
+Major Features and Improvements
+-------------------------------
+
+- Wheels for Python 3.9 have been added.
+- The ``flagser`` submodule has been updated to the latest upstream version, integrating the following changes:
+
+  - ``flagser`` now trows exceptions instead of exiting the computation;
+  - ``flagser`` now supports a number of threads as input parameter and, by default, it will use the maximum number of logic cores available.
+- ``flagser`` no longer produces output files.
+
+Bug Fixes
+---------
+
+An error encountered when running multiple instances of ``pyflagser`` in parallel (due to clashes between temporary file names) has been fixed.
+
+Backwards-Incompatible Changes
+------------------------------
+
+None.
+
+Thanks to our Contributors
+--------------------------
+
+This release contains contributions from many people:
+
+Julian Burella Pérez and Umberto Lupo.
+
+We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.
+
+
 Release 0.4.1
 =============
 
 Bug Fixes
 ---------
+
 A bug was fixed which caused some computations to hang when the prime for the finite field of coefficients used is greater than 2.
 
 Backwards-Incompatible Changes
 ------------------------------
+
 None.
 
 Thanks to our Contributors
@@ -24,6 +59,7 @@ Release 0.4.0
 
 Major Features and Improvements
 -------------------------------
+
 - ``flagser_count_unweighted`` and ``flagser_count_weighted`` were added to provide fast computations of simplex counts per dimension.
 - ``flagser_unweighted`` and ``flagser_weighted``'s performance was improved when ``coeff`` is 2 by using a compiled version of C++ ``flagser`` without the ``USE_COEFFICIENTS`` flag.
 - All C++ library files were moved to ``pyflagser/modules/`` upon compilation.
@@ -32,10 +68,12 @@ Major Features and Improvements
 
 Bug Fixes
 ---------
+
 - A bug was fixed which caused ``flagser_unweighted`` and ``flagser_weighted``'s output persistence diagrams to be of shape ``(0,)`` instead of ``(0, 2)`` if empty.
 
 Backwards-Incompatible Changes
 ------------------------------
+
 None.
 
 Thanks to our Contributors
@@ -53,16 +91,19 @@ Release 0.3.1
 
 Major Features and Improvements
 -------------------------------
+
 - Clarity of the code of ``flagser_unweighted`` and ``flagser_weighted`` was improved.
 - Auditwheel repair is now run in the manylinux jobs.
 - ``twine check`` is now run as part of the CI.
 
 Bug Fixes
 ---------
+
 - Fix bug causing ``flagser_weighted``'s output persistence diagrams to be a list of list of tuples instead of a list of ``numpy.ndarrays`` of shape (n_points, 2).
 
 Backwards-Incompatible Changes
 ------------------------------
+
 - Installation from tarballs is no longer supported.
 
 Thanks to our Contributors

azure-pipelines.yml

@@ -1,114 +1,6 @@
-# These jobs are triggered automatically and they test the code and the examples.
+# These jobs test the code and build the wheels and docs.
 
 jobs:
-- job: 'test_ubuntu1604'
-  condition: eq(variables['build_check'], 'false')
-  pool:
-    vmImage: 'ubuntu-16.04'
-  strategy:
-    matrix:
-      Python36:
-        python.version: '3.6'
-      Python37:
-        python.version: '3.7'
-      Python38:
-        python.version: '3.8'
-
-  steps:
-  - task: UsePythonVersion@0
-    inputs:
-      versionSpec: '$(python.version)'
-
-  - script: |
-      python -m pip install --upgrade pip setuptools
-    failOnStderr: true
-    displayName: 'Upgrade pip and setuptools'
-
-  - script: python -m pip install -e ".[tests, doc]"
-    failOnStderr: true
-    displayName: 'Install dev environment'
-
-  - script: |
-      pytest --cov pyflagser --cov-report xml
-      flake8
-    failOnStderr: true
-    displayName: 'Test with pytest and flake8'
-
-
-- job: 'test_macOS1014'
-  condition: eq(variables['build_check'], 'false')
-  pool:
-    vmImage: 'macOS-10.14'
-  strategy:
-    matrix:
-      Python36:
-        python.version: '3.6'
-      Python37:
-        python.version: '3.7'
-      Python38:
-        python.version: '3.8'
-
-  steps:
-  - task: UsePythonVersion@0
-    inputs:
-      versionSpec: '$(python.version)'
-
-  - script: |
-      python -m pip install --upgrade pip setuptools
-    failOnStderr: true
-    displayName: 'Upgrade pip and setuptools'
-
-  - script: python -m pip install -e ".[tests, doc]"
-    failOnStderr: true
-    displayName: 'Install dev environment'
-
-  - script: |
-      pytest --cov pyflagser --cov-report xml
-      flake8
-    failOnStderr: true
-    displayName: 'Test with pytest and flake8'
-
-
-- job: 'test_win2016'
-  condition: eq(variables['build_check'], 'false')
-  pool:
-    vmImage: 'vs2017-win2016'
-  strategy:
-    matrix:
-      Python36:
-        python_ver: '36'
-        python.version: '3.6'
-      Python37:
-        python_ver: '37'
-        python.version: '3.7'
-      Python38:
-        python_ver: '38'
-        python.version: '3.8'
-
-  steps:
-  - task: UsePythonVersion@0
-    inputs:
-      versionSpec: '$(python.version)'
-
-  - script: |
-      python -m python -m pip install --upgrade pip setuptools
-    failOnStderr: true
-    displayName: 'Upgrade pip and setuptools'
-
-  - script: |
-      python -m pip install -e ".[tests, doc]"
-    failOnStderr: true
-    displayName: 'Install dev environment'
-
-  - script: |
-      pytest --cov pyflagser --cov-report xml
-      flake8
-    failOnStderr: true
-    displayName: 'Test with pytest and flake8'
-
-
-# These jobs are triggered manually and they test the code and the examples and build the wheels and docs.
-
 - job: 'manylinux2010'
   condition: eq(variables['build_check'], 'true')
   pool:
@@ -130,6 +22,11 @@ jobs:
         plat: manylinux2010_x86_64
         python_ver: '38'
         python.version: '3.8'
+      Python39:
+        arch: x86_64
+        plat: manylinux2010_x86_64
+        python_ver: '39'
+        python.version: '3.9'
 
   steps:
   - task: UsePythonVersion@0
@@ -145,8 +42,8 @@ jobs:
     displayName: 'Run the docker, install and uninstall dev environment, test with pytest and flake8, build the wheels'
 
   - script: |
-      python -m pip install --upgrade pip
-    displayName: 'Upgrade pip and setuptools'
+      python -m pip install --upgrade pip setuptools wheel
+    displayName: 'Upgrade pip and setuptools, install wheel package'
 
   - script: python -m pip install dist/*.whl
     failOnStderr: true
@@ -158,6 +55,7 @@ jobs:
       cd tmp_test_cov
       python -m pyflagser.tests --webdl --no-cov --no-coverage-upload
     failOnStderr: true
+    condition: eq(variables['test_wheels'], 'true')
     displayName: 'Test the wheels with pytest'
 
   - task: CopyFiles@2
@@ -185,34 +83,40 @@ jobs:
         python.version: '3.7'
       Python38:
         python.version: '3.8'
+      Python39:
+        python.version: '3.9'
 
   steps:
   - task: UsePythonVersion@0
     inputs:
       versionSpec: '$(python.version)'
 
   - script: |
-      python -m pip install --upgrade pip setuptools
+      python -m pip install --upgrade pip setuptools wheel
     failOnStderr: true
-    displayName: 'Upgrade pip and setuptools'
+    displayName: 'Upgrade pip and setuptools, install wheel package'
 
   - script: python -m pip install -e ".[tests, doc]"
     failOnStderr: true
     displayName: 'Install dev environment'
 
   - script: |
-      pytest --cov pyflagser --cov-report xml
       flake8
     failOnStderr: true
-    displayName: 'Test with pytest and flake8'
+    displayName: 'Run flake8'
+
+  - script: |
+      pytest --cov pyflagser --cov-report xml
+    failOnStderr: true
+    displayName: 'Test dev install with pytest'
 
   - script: |
       pip uninstall -y pyflagser
     failOnStderr: true
     displayName: 'Uninstall pyflagser dev'
 
   - script: |
-      python -m pip install wheel
+      pip install wheel
       python setup.py bdist_wheel
     failOnStderr: false
     displayName: 'Build the wheels'
@@ -232,6 +136,7 @@ jobs:
       cd tmp_test_cov
       python -m pyflagser.tests --webdl --no-cov --no-coverage-upload
     failOnStderr: true
+    condition: eq(variables['test_wheels'], 'true')
     displayName: 'Test the wheels with pytest'
 
   - script: |
@@ -278,27 +183,29 @@ jobs:
       Python38:
         python_ver: '38'
         python.version: '3.8'
+      Python39:
+        python_ver: '39'
+        python.version: '3.9'
 
   steps:
   - task: UsePythonVersion@0
     inputs:
       versionSpec: '$(python.version)'
 
   - script: |
-      python -m pip install --upgrade pip setuptools
+      python -m pip install --upgrade pip setuptools wheel
     failOnStderr: true
-    displayName: 'Upgrade pip and setuptools'
+    displayName: 'Upgrade pip and setuptools, install wheel package'
 
   - script: |
       python -m pip install -e ".[tests, doc]"
     failOnStderr: true
     displayName: 'Install dev environment'
 
   - script: |
-      pytest --cov pyflagser --cov-report xml
-      flake8
+      pytest pyflagser --no-cov --no-coverage-upload
     failOnStderr: true
-    displayName: 'Test with pytest and flake8'
+    displayName: 'Test dev install with pytest'
 
   - script: |
       pip uninstall -y pyflagser
@@ -307,7 +214,7 @@ jobs:
 
   - bash: |
       sed -i $'s/\r$//' README.rst
-      python -m pip install wheel
+      pip install wheel
       python setup.py bdist_wheel
     failOnStderr: false
     displayName: 'Build the wheels'
@@ -321,6 +228,7 @@ jobs:
       cd tmp_test_cov
       python -m pyflagser.tests --webdl --no-cov --no-coverage-upload
     failOnStderr: true
+    condition: eq(variables['test_wheels'], 'true')
     displayName: 'Test the wheels with pytest'
 
   - task: CopyFiles@2

doc/index.rst

@@ -7,8 +7,8 @@ Welcome to pyflagser's API reference!
 =====================================
 
 
-:mod:`pyflagser`: Flag Complexes I/O and Persistence Homology
-=============================================================
+:mod:`pyflagser`: Flag Complexes I/O and Persistent Homology
+============================================================
 
 .. automodule:: pyflagser
    :no-members:

pyflagser/_version.py

@@ -17,4 +17,4 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = '0.4.1'
+__version__ = '0.4.2'