Release v0.4.1 (#47)

* Update flagser and bindings with latest build of flagser, fix #45 Arguments are now managed with a class instead of creating virtual command lines arguments. * Add regression test with coefficient higher than 2, to avoid #45 Add pytest-timeout to test suite and use it in test with higher coeffs * Bump version to 0.4.1 * Add release notes for 0.4.1 Signed-off-by: julian <[email protected]> Co-authored-by: Umberto Lupo <[email protected]> Co-authored-by: REDS institute <[email protected]>
giotto-ai · Sep 1, 2020 · 531589d · 531589d
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diff --git a/README.rst b/README.rst
@@ -1,5 +1,5 @@
-.. image:: https://www.giotto.ai/static/vector/logo.svg
-   :width: 850
+.. image:: https://raw.githubusercontent.com/giotto-ai/pyflagser/master/doc/images/Giotto_logo_RGB.svg
+   :width: 590
 
 |Azure|_ |Azure-cov|_ |Azure-test|_
 
@@ -22,53 +22,41 @@ pyflagser
 =========
 
 
-pyflagser s a python API for the flagser C++ library by Daniel Lütgehetmann which computes the homology of directed flag complexes. Please check out the original `luetge/flagser <https://github.com/luetge/flagser>`_ GitHub repository for more information.
-
-Website: https://giotto.ai
-
+``pyflagser`` is a python API for the flagser C++ library by Daniel Lütgehetmann which computes the homology of directed flag complexes. Please check out the original `luetge/flagser <https://github.com/luetge/flagser>`_ GitHub repository for more information.
 
 Project genesis
 ---------------
 
-pyflagser is the result of a collaborative effort between `L2F SA
-<https://www.l2f.ch/>`_, the `Laboratory for Topology and Neuroscience
-<https://www.epfl.ch/labs/hessbellwald-lab/>`_ at EPFL, and the `Institute of Reconfigurable & Embedded Digital Systems (REDS)
-<https://heig-vd.ch/en/research/reds>`_ of HEIG-VD.
+``pyflagser`` is the result of a collaborative effort between `L2F SA <https://www.l2f.ch/>`_, the `Laboratory for Topology and Neuroscience <https://www.epfl.ch/labs/hessbellwald-lab/>`_ at EPFL, and the `Institute of Reconfigurable & Embedded Digital Systems (REDS) <https://heig-vd.ch/en/research/reds>`_ of HEIG-VD.
 
 Installation
 ------------
 
 Dependencies
 ~~~~~~~~~~~~
 
-pyflagser requires:
+``pyflagser`` requires:
 
 - Python (>= 3.6)
-- numpy (>= 1.17.0)
-- scipy (>= 0.17.0)
-
-For running the examples jupyter, matplotlib and plotly are required.
+- NumPy (>= 1.17.0)
+- SciPy (>= 0.17.0)
 
 User installation
 ~~~~~~~~~~~~~~~~~
 
-If you already have a working installation of numpy and scipy,
-the easiest way to install pyflagser is using ``pip``   ::
+If you already have a working installation of numpy and scipy, the easiest way to install pyflagser is using ``pip``   ::
 
-    pip install -U pyflagser
+    python -m pip install -U pyflagser
 
 Documentation
 -------------
 
-- HTML documentation (stable release): https://docs-pyflagser.giotto.ai
+API reference (stable release): https://docs-pyflagser.giotto.ai
 
 Contributing
 ------------
 
-We welcome new contributors of all experience levels. The Giotto
-community goals are to be helpful, welcoming, and effective. To learn more about
-making a contribution to pyflagser, please see the `CONTRIBUTING.rst
-<https://github.com/giotto-ai/pyflagser/blob/master/CONTRIBUTING.rst>`_ file.
+We welcome new contributors of all experience levels. The Giotto community goals are to be helpful, welcoming, and effective. To learn more about making a contribution to ``pyflagser``, please see the `CONTRIBUTING.rst <https://github.com/giotto-ai/pyflagser/blob/master/CONTRIBUTING.rst>`_ file.
 
 Developer installation
 ~~~~~~~~~~~~~~~~~~~~~~
@@ -95,15 +83,14 @@ From the cloned repository's root directory, run
 
 .. code-block:: bash
 
-   pip install -e .
+   python -m pip install -e ".[tests]"
 
 This way, you can pull the library's latest changes and make them immediately available on your machine.
 
 Testing
 ~~~~~~~
 
-After installation, you can launch the test suite from outside the
-source directory::
+After installation, you can launch the test suite from outside the source directory::
 
     pytest pyflagser
 

diff --git a/RELEASE.rst b/RELEASE.rst
@@ -1,5 +1,26 @@
+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
+--------------------------
+
+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 0.4.0
-==============
+=============
 
 Major Features and Improvements
 -------------------------------
@@ -24,12 +45,11 @@ This release contains contributions from many people:
 
 Guillaume Tauzin, Umberto Lupo, and Julian Burella Pérez.
 
-We are also grateful to all who filed issues or helped resolve them, asked and
-answered questions, and were part of inspiring discussions.
+We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.
 
 
 Release 0.3.1
-==============
+=============
 
 Major Features and Improvements
 -------------------------------
@@ -52,8 +72,7 @@ This release contains contributions from many people:
 
 Umberto Lupo and Guillaume Tauzin.
 
-We are also grateful to all who filed issues or helped resolve them, asked and
-answered questions, and were part of inspiring discussions.
+We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.
 
 
 Release 0.3.0
@@ -124,12 +143,11 @@ This release contains contributions from many people:
 
 Guillaume Tauzin, Umberto Lupo, and Julian Burella Pérez.
 
-We are also grateful to all who filed issues or helped resolve them, asked and
-answered questions, and were part of inspiring discussions.
+We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.
 
 
 Release 0.2.1
-==============
+=============
 
 Major Features and Improvements
 -------------------------------
@@ -158,12 +176,11 @@ This release contains contributions from many people:
 
 Julian Burella Pérez, Umberto Lupo, and Guillaume Tauzin.
 
-We are also grateful to all who filed issues or helped resolve them, asked and
-answered questions, and were part of inspiring discussions.
+We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.
 
 
 Release 0.2.0
-==============
+=============
 
 Major Features and Improvements
 -------------------------------
@@ -187,12 +204,11 @@ This release contains contributions from many people:
 
 Julian Burella Pérez, Umberto Lupo, and Guillaume Tauzin.
 
-We are also grateful to all who filed issues or helped resolve them, asked and
-answered questions, and were part of inspiring discussions.
+We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.
 
 
 Release 0.1.0
-==============
+=============
 
 Initial release of ``pyflagser``.
 
@@ -220,5 +236,4 @@ This release contains contributions from many people:
 
 Guillaume Tauzin, 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.
+We are also grateful to all who filed issues or helped resolve them, asked and answered questions, and were part of inspiring discussions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -24,7 +24,7 @@ jobs:
     failOnStderr: true
     displayName: 'Upgrade pip and setuptools'
 
-  - script: pip install -e ".[tests, doc]"
+  - script: python -m pip install -e ".[tests, doc]"
     failOnStderr: true
     displayName: 'Install dev environment'
 
@@ -58,7 +58,7 @@ jobs:
     failOnStderr: true
     displayName: 'Upgrade pip and setuptools'
 
-  - script: pip install -e ".[tests, doc]"
+  - script: python -m pip install -e ".[tests, doc]"
     failOnStderr: true
     displayName: 'Install dev environment'
 
@@ -91,12 +91,12 @@ jobs:
       versionSpec: '$(python.version)'
 
   - script: |
-      python -m pip install --upgrade pip setuptools
+      python -m python -m pip install --upgrade pip setuptools
     failOnStderr: true
     displayName: 'Upgrade pip and setuptools'
 
   - script: |
-      pip install -e ".[tests, doc]"
+      python -m pip install -e ".[tests, doc]"
     failOnStderr: true
     displayName: 'Install dev environment'
 
@@ -148,12 +148,12 @@ jobs:
       python -m pip install --upgrade pip
     displayName: 'Upgrade pip and setuptools'
 
-  - script: pip install dist/*.whl
+  - script: python -m pip install dist/*.whl
     failOnStderr: true
     displayName: 'Install the wheels'
 
   - script: |
-      pip install pytest pytest-cov pytest-azurepipelines pytest-benchmark flake8 hypothesis
+      python -m pip install pytest pytest-cov pytest-timeout pytest-azurepipelines pytest-benchmark flake8 hypothesis
       mkdir tmp_test_cov
       cd tmp_test_cov
       python -m pyflagser.tests --webdl --no-cov --no-coverage-upload
@@ -196,7 +196,7 @@ jobs:
     failOnStderr: true
     displayName: 'Upgrade pip and setuptools'
 
-  - script: pip install -e ".[tests, doc]"
+  - script: python -m pip install -e ".[tests, doc]"
     failOnStderr: true
     displayName: 'Install dev environment'
 
@@ -212,18 +212,18 @@ jobs:
     displayName: 'Uninstall pyflagser dev'
 
   - script: |
-      pip install wheel
+      python -m pip install wheel
       python setup.py bdist_wheel
     failOnStderr: false
     displayName: 'Build the wheels'
 
   - script: |
       set -e
-      pip install twine
+      python -m pip install twine
       twine check dist/*
     displayName: 'Check distribution with twine'
 
-  - script: pip install dist/*.whl
+  - script: python -m pip install dist/*.whl
     failOnStderr: true
     displayName: 'Install the wheels'
 
@@ -290,7 +290,7 @@ jobs:
     displayName: 'Upgrade pip and setuptools'
 
   - script: |
-      pip install -e ".[tests, doc]"
+      python -m pip install -e ".[tests, doc]"
     failOnStderr: true
     displayName: 'Install dev environment'
 
@@ -307,12 +307,12 @@ jobs:
 
   - bash: |
       sed -i $'s/\r$//' README.rst
-      pip install wheel
+      python -m pip install wheel
       python setup.py bdist_wheel
     failOnStderr: false
     displayName: 'Build the wheels'
 
-  - bash: pip install dist/*.whl
+  - bash: python -m pip install dist/*.whl
     failOnStderr: true
     displayName: 'Install the wheels'
 

diff --git a/doc/images/Giotto_logo_RGB.svg b/doc/images/Giotto_logo_RGB.svg
diff --git a/flagser b/flagser
diff --git a/pyflagser/_version.py b/pyflagser/_version.py
@@ -17,4 +17,4 @@
 # 'X.Y.dev0' is the canonical version of 'X.Y.dev'
 #
 
-__version__ = '0.4.0'
+__version__ = '0.4.1'
+7 −10		include/complex/directed_flag_complex_computer.h
+1 −0		include/complex/directed_flag_complex_in_memory.h
+4 −8		include/complex/directed_flag_complex_in_memory_computer.h
+3 −3		include/input/flagser.h
+8 −7		include/input/h5.h
+8 −12		include/input/input_classes.h
+5 −6		include/output/barcode.h
+7 −9		include/output/barcode_hdf5.h
+1 −4		include/output/base.h
+7 −8		include/output/betti.h
+4 −4		include/output/hdf5.h
+6 −16		include/output/output_classes.h
+6 −7		include/output/trivial.h
+77 −0		include/parameters.h
+10 −9		src/flagser-count.cpp
+16 −30		src/flagser.cpp
+6 −21		src/ripser.cpp
+77 −74		test/base.h