Create giotto-tda v0.3.1 (#536)

* Add workflow figure to docs (#519)

* Add workflow figure to docs

* Fix forgotten reshape in MNIST notebook

* Add 0.3.0 to the list of versions

Co-authored-by: wreise <[email protected]>

* Upload new mapper pipeline svg (#521)

* Fix copyright notices (#522)

* 🎨 Clean up shape classification tutorial (#523)

* Add subsection to improve baseline model, remove projective space subsection

* Remove case study prefix from Lorenz attractor example

Co-authored-by: wreise <[email protected]>
Co-authored-by: Umberto Lupo <[email protected]>

* [CI] Rename notebooks_check to test_notebooks and add test_wheels variable (#524)

* Update PairwiseDistance docstring for bottleneck distance (#525)

Update the docstring to state what could happen with the symmetry of the bottleneck distance when the delta parameter is non-zero

* Bump macOS version in Azure jobs to 10.15 (#527)

* Bump macOS version in Azure jobs to 10.15

Attempt to fix the brew woes in the Azure jobs by trying the suggestion in https://developercommunity.visualstudio.com/comments/1239467/view.html

* Increase timeout deadline to 500ms in some flaky tests (#531)

* Increase timeout deadline to 500ms in collapser and mapper clustering classes tests

* Use list comprehensions in _time_delay_embedding

* Pull ripser.py latest changes (#530)

* Update ripser.py commit

* Add robinhhood hashmap as a dependency

* Enable use of robinhood hashmap for ripser

* Update ccache on azure pipeline

Signed-off-by: julian <[email protected]>

* Split time series classification notebook into two (#529)

* Separate the two notebooks

* Rename time_series_classification notebook to topology_time_series

* Revert #465 following #530

* Use np.asarray to handle coo attributes being lists

* Fix documentation after splitting time series classification notebook (#533)

* Add gravitational waves notebook to docs, rename time_series_classification to topology_time_series following #529

* Change link to use cases on giotto.ai

* Clarify situation with use cases needing old versions of the library

Co-authored-by: Umberto Lupo <[email protected]>

* Add copyright notice inherited from ripser.py following @MonkeyBreaker's comment

* Prepare for v0.3.1 (#534)

* Bump version number to 0.3.1

* Make release notes for 0.3.1 and add @rorondre to code authors

Co-authored-by: wreise <[email protected]>

Co-authored-by: wreise <[email protected]>
Co-authored-by: lewtun <[email protected]>
Co-authored-by: rorondre <[email protected]>
Co-authored-by: REDS institute <[email protected]>
Co-authored-by: Wojciech Reise <[email protected]>

.gitmodules

@@ -14,3 +14,6 @@
 [submodule "gtda/externals/pybind11"]
 	path = gtda/externals/pybind11
 	url = https://github.com/pybind/pybind11
+[submodule "gtda/externals/robinhood"]
+	path = gtda/externals/robinhood
+	url = https://github.com/martinus/robin-hood-hashing

CMakeLists.txt

@@ -13,6 +13,7 @@ set(RIPSER_SRC_DIR "gtda/externals/ripser")
 set(GUDHI_SRC_DIR "gtda/externals/gudhi-devel/src")
 set(HERA_DIR "gtda/externals/hera")
 set(EIGEN_DIR "gtda/externals/eigen")
+set(ROBINHOOD_DIR "gtda/externals/robinhood")
 
 #######################################################################
 #                               Ripser                                #
@@ -27,6 +28,8 @@ endif()
 
 target_compile_definitions(gtda_ripser PRIVATE ASSEMBLE_REDUCTION_MATRIX=1)
 target_include_directories(gtda_ripser PRIVATE "${RIPSER_SRC_DIR}/ripser")
+target_compile_definitions(gtda_ripser PRIVATE USE_ROBINHOOD_HASHMAP=1)
+target_include_directories(gtda_ripser PRIVATE "${ROBINHOOD_DIR}/src/include")
 
 if(MSVC)
     target_compile_options(gtda_ripser PUBLIC $<$<CONFIG:RELEASE>: /Wall /O2>)
@@ -49,6 +52,8 @@ endif()
 
 target_compile_definitions(gtda_ripser_coeff PRIVATE USE_COEFFICIENTS=1 ASSEMBLE_REDUCTION_MATRIX=1)
 target_include_directories(gtda_ripser_coeff PRIVATE "${RIPSER_SRC_DIR}/ripser")
+target_compile_definitions(gtda_ripser_coeff PRIVATE USE_ROBINHOOD_HASHMAP=1)
+target_include_directories(gtda_ripser_coeff PRIVATE "${ROBINHOOD_DIR}/src/include")
 
 if(MSVC)
     target_compile_options(gtda_ripser_coeff PUBLIC $<$<CONFIG:RELEASE>: /Wall /O2>)

CODE_AUTHORS.rst

@@ -14,3 +14,4 @@ Where component authors are known, add them here.
 | Wojciech Reise, [email protected]
 | Roman Yurchak, [email protected]
 | Nick Sale, [email protected]
+| Rayna Andreeva, [email protected]

LICENSE

@@ -1,4 +1,4 @@
-Copyright 2019 L2F SA.
+Copyright 2020 L2F SA.
 
 If you need a different distribution license, please contact the L2F team
 at [email protected].

azure-pipelines.yml

@@ -41,7 +41,7 @@ jobs:
 
   - task: Cache@2
     inputs:
-      key: '"ccache-wheels-v2020.10.05" | $(Agent.OS) | "$(python.version)"'
+      key: '"ccache-wheels-v2020.11.03" | $(Agent.OS) | "$(python.version)"'
       path: $(CCACHE_DIR)
     displayName: ccache
 
@@ -73,6 +73,7 @@ jobs:
       mkdir tmp_test_cov
       cd tmp_test_cov
       pytest --pyargs gtda --ignore-glob='*externals*' --no-cov --no-coverage-upload
+    condition: eq(variables['test_wheels'], 'true')
     displayName: 'Test the wheels with pytest'
 
   - script: |
@@ -84,7 +85,7 @@ jobs:
       do
         papermill --start_timeout 2000 $n -
       done
-    condition: eq(variables['notebooks_check'], 'true')
+    condition: eq(variables['test_notebooks'], 'true')
     displayName: 'Test jupyter notebooks with papermill'
 
   - task: CopyFiles@2
@@ -107,9 +108,9 @@ jobs:
     displayName: 'Upload nightly wheels to PyPI'
 
 
-- job: 'macOS1014'
+- job: 'macOS1015'
   pool:
-    vmImage: 'macOS-10.14'
+    vmImage: 'macOS-10.15'
   strategy:
     matrix:
       Python36:
@@ -138,7 +139,7 @@ jobs:
 
   - task: Cache@2
     inputs:
-      key: '"ccache-v2020.10.05" | $(Agent.OS) | "$(python.version)"'
+      key: '"ccache-v2020.11.03" | $(Agent.OS) | "$(python.version)"'
       path: $(CCACHE_DIR)
     displayName: ccache
 
@@ -170,8 +171,8 @@ jobs:
 
   - script: |
       set -e
-      pip uninstall -y giotto-tda
-      pip uninstall -y giotto-tda-nightly
+      python -m pip uninstall -y giotto-tda
+      python -m pip uninstall -y giotto-tda-nightly
     displayName: 'Uninstall giotto-tda/giotto-tda-nightly'
 
   - script: |
@@ -187,6 +188,7 @@ jobs:
       mkdir tmp_test_cov
       cd tmp_test_cov
       pytest --pyargs gtda --ignore-glob='*externals*' --no-cov --no-coverage-upload
+    condition: eq(variables['test_wheels'], 'true')
     displayName: 'Test the wheels with pytest'
 
   - script: |
@@ -198,7 +200,7 @@ jobs:
       do
         papermill --start_timeout 2000 $n -
       done
-    condition: eq(variables['notebooks_check'], 'true')
+    condition: eq(variables['test_notebooks'], 'true')
     displayName: 'Test jupyter notebooks with papermill'
 
   - task: CopyFiles@2
@@ -273,7 +275,7 @@ jobs:
   - script: |
       python -m pip uninstall -y giotto-tda
       python -m pip uninstall -y giotto-tda-nightly
-    displayName: 'Uninstall giotto-tda/giotto-tda-nightly dev'
+    displayName: 'Uninstall giotto-tda/giotto-tda-nightly'
 
   - bash: |
       set -e
@@ -288,14 +290,15 @@ jobs:
       mkdir tmp_test_cov
       cd tmp_test_cov
       pytest --pyargs gtda --ignore-glob='*externals*' --no-cov --no-coverage-upload
+    condition: eq(variables['test_wheels'], 'true')
     displayName: 'Test the wheels with pytest'
 
   - script: |
       python -m pip install -e ".[examples]"
       python -m pip install papermill
       cd examples
       FOR %%n in (*.ipynb) DO (papermill --start_timeout 2000 %%n - || exit /b)
-    condition: eq(variables['notebooks_check'], 'true')
+    condition: eq(variables['test_notebooks'], 'true')
     displayName: 'Test jupyter notebooks with papermill'
 
   - task: CopyFiles@2

doc/conf.py

@@ -21,7 +21,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'giotto-tda'
-copyright = '2020, L2F'
+copyright = '2020, L2F SA'
 author = 'Guillaume Tauzin, Umberto Lupo, Matteo Caorsi, Anibal Medina, ' \
          'Lewis Tunstall, Wojciech Reise'