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 <wojciech.reise@epfl.ch> * 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 <wojciech.reise@epfl.ch> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com> * [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 <julian.burellaperez@heig-vd.ch> * 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 <umberto.lupo@gmail.com> * 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 <wojciech.reise@epfl.ch> Co-authored-by: wreise <wojciech.reise@epfl.ch> Co-authored-by: lewtun <lewis.c.tunstall@gmail.com> Co-authored-by: rorondre <r.andreeva@sms.ed.ac.uk> Co-authored-by: REDS institute <reds-heig@users.noreply.github.com> Co-authored-by: Wojciech Reise <32167173+wreise@users.noreply.github.com>
giotto-ai · Nov 20, 2020 · 14d388d · 14d388d
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commit 14d388d
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Showing 38 changed files with 3,040 additions and 2,539 deletions.
diff --git a/.gitmodules b/.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
diff --git a/CMakeLists.txt b/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>)

diff --git a/CODE_AUTHORS.rst b/CODE_AUTHORS.rst
@@ -14,3 +14,4 @@ Where component authors are known, add them here.
 | Wojciech Reise, reisewojciech@gmail.com
 | Roman Yurchak, roman.yurchak@symerio.com
 | Nick Sale, nicholas.j.sale@gmail.com
+| Rayna Andreeva, r.andreeva@sms.ed.ac.uk
diff --git a/LICENSE b/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 business@l2f.ch.

diff --git a/azure-pipelines.yml b/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

diff --git a/doc/conf.py b/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'
 

diff --git a/doc/images/giotto-tda_workflow.png b/doc/images/giotto-tda_workflow.png