From b3b8af2e12ec81924fc6e6c405fdee1c82b02a65 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Fri, 1 May 2020 18:36:20 +0200 Subject: [PATCH 01/21] Improved docs and changed scipy version --- README.md | 2 +- .../plot_free_support_barycenter.py | 6 +- examples/domain-adaptation/plot_otda_d2.py | 2 +- .../domain-adaptation/plot_otda_mapping.py | 4 +- .../plot_otda_mapping_colors_images.py | 1 + examples/gromov/plot_barycenter_fgw.py | 11 +- examples/gromov/plot_fgw.py | 10 +- examples/plot_compute_emd.py | 4 +- examples/plot_optim_OTreg.py | 6 +- examples/plot_screenkhorn_1D.py | 7 +- examples/plot_stochastic.py | 101 +++++++----------- requirements.txt | 2 +- setup.py | 2 +- 13 files changed, 72 insertions(+), 86 deletions(-) diff --git a/README.md b/README.md index b9b8f4576..51fc02273 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ year={2017} The library has been tested on Linux, MacOSX and Windows. It requires a C++ compiler for building/installing the EMD solver and relies on the following Python modules: - Numpy (>=1.11) -- Scipy (>=1.0) +- Scipy (>=1.3) - Cython (>=0.23) - Matplotlib (>=1.5) diff --git a/examples/barycenters/plot_free_support_barycenter.py b/examples/barycenters/plot_free_support_barycenter.py index 64b89e4fc..27ddc8e77 100644 --- a/examples/barycenters/plot_free_support_barycenter.py +++ b/examples/barycenters/plot_free_support_barycenter.py @@ -4,7 +4,7 @@ 2D free support Wasserstein barycenters of distributions ==================================================== -Illustration of 2D Wasserstein barycenters if discributions that are weighted +Illustration of 2D Wasserstein barycenters if distributions are weighted sum of diracs. """ @@ -21,7 +21,7 @@ ############################################################################## # Generate data # ------------- -#%% parameters and data generation + N = 3 d = 2 measures_locations = [] @@ -46,7 +46,7 @@ ############################################################################## # Compute free support barycenter -# ------------- +# ------------------------------- k = 10 # number of Diracs of the barycenter X_init = np.random.normal(0., 1., (k, d)) # initial Dirac locations diff --git a/examples/domain-adaptation/plot_otda_d2.py b/examples/domain-adaptation/plot_otda_d2.py index f49a57092..d8b2a9350 100644 --- a/examples/domain-adaptation/plot_otda_d2.py +++ b/examples/domain-adaptation/plot_otda_d2.py @@ -25,7 +25,7 @@ import ot.plot ############################################################################## -# generate data +# Generate data # ------------- n_samples_source = 150 diff --git a/examples/domain-adaptation/plot_otda_mapping.py b/examples/domain-adaptation/plot_otda_mapping.py index ded2bdf85..d21d3c94c 100644 --- a/examples/domain-adaptation/plot_otda_mapping.py +++ b/examples/domain-adaptation/plot_otda_mapping.py @@ -9,8 +9,8 @@ a linear or a kernelized mapping as introduced in [8]. [8] M. Perrot, N. Courty, R. Flamary, A. Habrard, - "Mapping estimation for discrete optimal transport", - Neural Information Processing Systems (NIPS), 2016. +"Mapping estimation for discrete optimal transport", +Neural Information Processing Systems (NIPS), 2016. """ # Authors: Remi Flamary diff --git a/examples/domain-adaptation/plot_otda_mapping_colors_images.py b/examples/domain-adaptation/plot_otda_mapping_colors_images.py index 9d3a7c7ba..ee5c8b0f8 100644 --- a/examples/domain-adaptation/plot_otda_mapping_colors_images.py +++ b/examples/domain-adaptation/plot_otda_mapping_colors_images.py @@ -9,6 +9,7 @@ [6] Ferradans, S., Papadakis, N., Peyre, G., & Aujol, J. F. (2014). Regularized discrete optimal transport. SIAM Journal on Imaging Sciences, 7(3), 1853-1882. + [8] M. Perrot, N. Courty, R. Flamary, A. Habrard, "Mapping estimation for discrete optimal transport", Neural Information Processing Systems (NIPS), 2016. diff --git a/examples/gromov/plot_barycenter_fgw.py b/examples/gromov/plot_barycenter_fgw.py index 77b037089..3f8176530 100644 --- a/examples/gromov/plot_barycenter_fgw.py +++ b/examples/gromov/plot_barycenter_fgw.py @@ -4,14 +4,15 @@ Plot graphs' barycenter using FGW ================================= -This example illustrates the computation barycenter of labeled graphs using FGW +This example illustrates the computation barycenter of labeled graphs using +FGW [18]. Requires networkx >=2 -.. [18] Vayer Titouan, Chapel Laetitia, Flamary R{\'e}mi, Tavenard Romain - and Courty Nicolas - "Optimal Transport for structured data with application on graphs" - International Conference on Machine Learning (ICML). 2019. +[18] Vayer Titouan, Chapel Laetitia, Flamary Rémi, Tavenard Romain +and Courty Nicolas +"Optimal Transport for structured data with application on graphs" +International Conference on Machine Learning (ICML). 2019. """ diff --git a/examples/gromov/plot_fgw.py b/examples/gromov/plot_fgw.py index 73e486e0e..97fe6191d 100644 --- a/examples/gromov/plot_fgw.py +++ b/examples/gromov/plot_fgw.py @@ -4,12 +4,12 @@ Plot Fused-gromov-Wasserstein ============================== -This example illustrates the computation of FGW for 1D measures[18]. +This example illustrates the computation of FGW for 1D measures [18]. -.. [18] Vayer Titouan, Chapel Laetitia, Flamary R{\'e}mi, Tavenard Romain - and Courty Nicolas - "Optimal Transport for structured data with application on graphs" - International Conference on Machine Learning (ICML). 2019. +[18] Vayer Titouan, Chapel Laetitia, Flamary Rémi, Tavenard Romain +and Courty Nicolas +"Optimal Transport for structured data with application on graphs" +International Conference on Machine Learning (ICML). 2019. """ diff --git a/examples/plot_compute_emd.py b/examples/plot_compute_emd.py index 334011538..527a847ad 100644 --- a/examples/plot_compute_emd.py +++ b/examples/plot_compute_emd.py @@ -4,8 +4,8 @@ Plot multiple EMD ================= -Shows how to compute multiple EMD and Sinkhorn with two differnt -ground metrics and plot their values for diffeent distributions. +Shows how to compute multiple EMD and Sinkhorn with two different +ground metrics and plot their values for different distributions. """ diff --git a/examples/plot_optim_OTreg.py b/examples/plot_optim_OTreg.py index 51e2fdca9..5eb15bdb9 100644 --- a/examples/plot_optim_OTreg.py +++ b/examples/plot_optim_OTreg.py @@ -6,7 +6,7 @@ Illustrates the use of the generic solver for regularized OT with user-designed regularization term. It uses Conditional gradient as in [6] and -generalized Conditional Gradient as proposed in [5][7]. +generalized Conditional Gradient as proposed in [5,7]. [5] N. Courty; R. Flamary; D. Tuia; A. Rakotomamonjy, Optimal Transport for @@ -14,8 +14,8 @@ Intelligence , vol.PP, no.99, pp.1-1. [6] Ferradans, S., Papadakis, N., Peyré, G., & Aujol, J. F. (2014). -Regularized discrete optimal transport. SIAM Journal on Imaging Sciences, -7(3), 1853-1882. +Regularized discrete optimal transport. SIAM Journal on Imaging +Sciences, 7(3), 1853-1882. [7] Rakotomamonjy, A., Flamary, R., & Courty, N. (2015). Generalized conditional gradient: analysis of convergence and applications. diff --git a/examples/plot_screenkhorn_1D.py b/examples/plot_screenkhorn_1D.py index 840ead848..785642ab1 100644 --- a/examples/plot_screenkhorn_1D.py +++ b/examples/plot_screenkhorn_1D.py @@ -4,8 +4,11 @@ 1D Screened optimal transport =============================== -This example illustrates the computation of Screenkhorn: -Screening Sinkhorn Algorithm for Optimal transport. +This example illustrates the computation of Screenkhorn [26]. + +[26] Alaya M. Z., Bérar M., Gasso G., Rakotomamonjy A. (2019). +Screening Sinkhorn Algorithm for Regularized Optimal Transport, +Advances in Neural Information Processing Systems 33 (NeurIPS). """ # Author: Mokhtar Z. Alaya diff --git a/examples/plot_stochastic.py b/examples/plot_stochastic.py index 742f8d9ef..3a1ef3167 100644 --- a/examples/plot_stochastic.py +++ b/examples/plot_stochastic.py @@ -1,10 +1,18 @@ """ -========================== +=================== Stochastic examples -========================== +=================== This example is designed to show how to use the stochatic optimization -algorithms for descrete and semicontinous measures from the POT library. +algorithms for discrete and semi-continuous measures from the POT library. + +[18] Genevay, A., Cuturi, M., Peyré, G. & Bach, F. +Stochastic Optimization for Large-scale Optimal Transport. +Advances in Neural Information Processing Systems (2016). + +[19] Seguy, V., Bhushan Damodaran, B., Flamary, R., Courty, N., Rolet, A. & +Blondel, M. Large-scale Optimal Transport and Mapping Estimation. +International Conference on Learning Representation (2018) """ @@ -19,16 +27,14 @@ ############################################################################# -# COMPUTE TRANSPORTATION MATRIX FOR SEMI-DUAL PROBLEM -############################################################################# -############################################################################# -# DISCRETE CASE: +# Compute the Transportation Matrix for the Semi-Dual Problem +# ----------------------------------------------------------- # -# Sample two discrete measures for the discrete case -# --------------------------------------------- +# Discrete case +# ````````````` # -# Define 2 discrete measures a and b, the points where are defined the source -# and the target measures and finally the cost matrix c. +# Sample two discrete measures for the discrete case and compute their cost +# matrix c. n_source = 7 n_target = 4 @@ -44,12 +50,7 @@ M = ot.dist(X_source, Y_target) ############################################################################# -# # Call the "SAG" method to find the transportation matrix in the discrete case -# --------------------------------------------- -# -# Define the method "SAG", call ot.solve_semi_dual_entropic and plot the -# results. method = "SAG" sag_pi = ot.stochastic.solve_semi_dual_entropic(a, b, M, reg, method, @@ -57,14 +58,12 @@ print(sag_pi) ############################################################################# -# SEMICONTINOUS CASE: +# Semi-Continuous Case +# ```````````````````` # # Sample one general measure a, one discrete measures b for the semicontinous -# case -# --------------------------------------------- -# -# Define one general measure a, one discrete measures b, the points where -# are defined the source and the target measures and finally the cost matrix c. +# case, the points where source and target measures are defined and compute the +# cost matrix. n_source = 7 n_target = 4 @@ -81,13 +80,8 @@ M = ot.dist(X_source, Y_target) ############################################################################# -# # Call the "ASGD" method to find the transportation matrix in the semicontinous -# case -# --------------------------------------------- -# -# Define the method "ASGD", call ot.solve_semi_dual_entropic and plot the -# results. +# case. method = "ASGD" asgd_pi, log_asgd = ot.stochastic.solve_semi_dual_entropic(a, b, M, reg, method, @@ -96,23 +90,17 @@ print(asgd_pi) ############################################################################# -# # Compare the results with the Sinkhorn algorithm -# --------------------------------------------- -# -# Call the Sinkhorn algorithm from POT sinkhorn_pi = ot.sinkhorn(a, b, M, reg) print(sinkhorn_pi) ############################################################################## -# PLOT TRANSPORTATION MATRIX -############################################################################## - -############################################################################## -# Plot SAG results -# ---------------- +# Plot Transportation Matrices +# ```````````````````````````` +# +# For SAG pl.figure(4, figsize=(5, 5)) ot.plot.plot1D_mat(a, b, sag_pi, 'semi-dual : OT matrix SAG') @@ -120,8 +108,7 @@ ############################################################################## -# Plot ASGD results -# ----------------- +# For ASGD pl.figure(4, figsize=(5, 5)) ot.plot.plot1D_mat(a, b, asgd_pi, 'semi-dual : OT matrix ASGD') @@ -129,8 +116,7 @@ ############################################################################## -# Plot Sinkhorn results -# --------------------- +# For Sinkhorn pl.figure(4, figsize=(5, 5)) ot.plot.plot1D_mat(a, b, sinkhorn_pi, 'OT matrix Sinkhorn') @@ -138,17 +124,14 @@ ############################################################################# -# COMPUTE TRANSPORTATION MATRIX FOR DUAL PROBLEM -############################################################################# -############################################################################# -# SEMICONTINOUS CASE: +# Compute the Transportation Matrix for the Dual Problem +# ------------------------------------------------------ # -# Sample one general measure a, one discrete measures b for the semicontinous -# case -# --------------------------------------------- +# Semi-continuous case +# ```````````````````` # -# Define one general measure a, one discrete measures b, the points where -# are defined the source and the target measures and finally the cost matrix c. +# Sample one general measure a, one discrete measures b for the semi-continuous +# case and compute the cost matrix c. n_source = 7 n_target = 4 @@ -169,10 +152,7 @@ ############################################################################# # # Call the "SGD" dual method to find the transportation matrix in the -# semicontinous case -# --------------------------------------------- -# -# Call ot.solve_dual_entropic and plot the results. +# semi-continuous case sgd_dual_pi, log_sgd = ot.stochastic.solve_dual_entropic(a, b, M, reg, batch_size, numItermax, @@ -183,7 +163,7 @@ ############################################################################# # # Compare the results with the Sinkhorn algorithm -# --------------------------------------------- +# ``````````````````````````````````````````````` # # Call the Sinkhorn algorithm from POT @@ -191,8 +171,10 @@ print(sinkhorn_pi) ############################################################################## -# Plot SGD results -# ----------------- +# Plot Transportation Matrices +# ```````````````````````````` +# +# For SGD pl.figure(4, figsize=(5, 5)) ot.plot.plot1D_mat(a, b, sgd_dual_pi, 'dual : OT matrix SGD') @@ -200,8 +182,7 @@ ############################################################################## -# Plot Sinkhorn results -# --------------------- +# For Sinkhorn pl.figure(4, figsize=(5, 5)) ot.plot.plot1D_mat(a, b, sinkhorn_pi, 'OT matrix Sinkhorn') diff --git a/requirements.txt b/requirements.txt index bee22f7ab..331dd570a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ numpy -scipy>=1.0 +scipy>=1.3 cython matplotlib autograd diff --git a/setup.py b/setup.py index 4640d00c1..5932ce9c6 100755 --- a/setup.py +++ b/setup.py @@ -66,7 +66,7 @@ license='MIT', scripts=[], data_files=[], - requires=["numpy", "scipy", "cython"], + requires=["numpy", "scipy>=1.3", "cython"], install_requires=["numpy", "scipy", "cython"], classifiers=[ 'Development Status :: 5 - Production/Stable', From ed320834f93b1e83bef2fee03ab664722f16b1e5 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Fri, 1 May 2020 18:55:57 +0200 Subject: [PATCH 02/21] Fixed dependency bug in setup.py --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 5932ce9c6..3f658923a 100755 --- a/setup.py +++ b/setup.py @@ -66,8 +66,8 @@ license='MIT', scripts=[], data_files=[], - requires=["numpy", "scipy>=1.3", "cython"], - install_requires=["numpy", "scipy", "cython"], + requires=["numpy", "scipy", "cython"], + install_requires=["numpy", "scipy>=1.3", "cython"], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Developers', From ed6b3b120447aa3db268b8a1e8c26bf42cb443e1 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Fri, 1 May 2020 22:57:21 +0200 Subject: [PATCH 03/21] dependencies set to minimal versions for tests --- .github/workflows/pythonpackage.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 079205904..1b7599ee6 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -28,7 +28,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r requirements.txt + pip install -r .github/requirements_strict.txt pip install flake8 pytest "pytest-cov<2.6" codecov pip install -U "sklearn" - name: Lint with flake8 @@ -64,7 +64,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r requirements.txt + pip install -r .github/requirements_strict.txt pip install pytest "pytest-cov<2.6" pip install -U "sklearn" - name: Install POT @@ -91,7 +91,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r requirements.txt + pip install -r .github/requirements_strict.txt pip install pytest "pytest-cov<2.6" pip install -U "sklearn" - name: Install POT From 5a3452dad1dad143c8375c5ae3366009733de491 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Fri, 1 May 2020 23:02:38 +0200 Subject: [PATCH 04/21] add requirements file --- .github/requirements_strict.txt | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 .github/requirements_strict.txt diff --git a/.github/requirements_strict.txt b/.github/requirements_strict.txt new file mode 100644 index 000000000..e9e6ca4f6 --- /dev/null +++ b/.github/requirements_strict.txt @@ -0,0 +1,10 @@ +numpy==1.11.* +scipy==1.3.* +cython==0.23.* +matplotlib==1.5.* +autograd +pymanopt==0.2.4; python_version <'3' +pymanopt; python_version >= '3' +cvxopt +scikit-learn +pytest From 501795fd50785788c51f77f60d7722fdd6c6d758 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Sun, 3 May 2020 14:29:21 +0200 Subject: [PATCH 05/21] added minimal version build for scipy (testing 1.2) --- .github/requirements_strict.txt | 8 +++--- .github/workflows/pythonpackage.yml | 43 +++++++++++++++++++++++++++-- 2 files changed, 44 insertions(+), 7 deletions(-) diff --git a/.github/requirements_strict.txt b/.github/requirements_strict.txt index e9e6ca4f6..43ca36814 100644 --- a/.github/requirements_strict.txt +++ b/.github/requirements_strict.txt @@ -1,7 +1,7 @@ -numpy==1.11.* -scipy==1.3.* -cython==0.23.* -matplotlib==1.5.* +numpy +scipy==1.2.* +cython +matplotlib autograd pymanopt==0.2.4; python_version <'3' pymanopt; python_version >= '3' diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 1b7599ee6..b39c48d85 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -28,7 +28,44 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r .github/requirements_strict.txt + pip install -r requirements.txt + pip install flake8 pytest "pytest-cov<2.6" codecov + pip install -U "sklearn" + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics + - name: Install POT + run: | + pip install -e . + - name: Run tests + run: | + python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot + - name: Upload codecov + run: | + codecov + + + linux-minimal-deps: + + runs-on: ubuntu-latest + strategy: + max-parallel: 4 + matrix: + python-version: [3.5, 3.6, 3.7, 3.8] + + steps: + - uses: actions/checkout@v1 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r requirements_strict.txt pip install flake8 pytest "pytest-cov<2.6" codecov pip install -U "sklearn" - name: Lint with flake8 @@ -64,7 +101,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r .github/requirements_strict.txt + pip install -r requirements.txt pip install pytest "pytest-cov<2.6" pip install -U "sklearn" - name: Install POT @@ -91,7 +128,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r .github/requirements_strict.txt + pip install -r requirements.txt pip install pytest "pytest-cov<2.6" pip install -U "sklearn" - name: Install POT From 0a88bfac95a8ca50b9612e970a9975bbef5996a0 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Sun, 3 May 2020 14:30:49 +0200 Subject: [PATCH 06/21] bugfix in minimal deps build --- .github/workflows/pythonpackage.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index b39c48d85..5ed06e4fb 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -54,7 +54,7 @@ jobs: strategy: max-parallel: 4 matrix: - python-version: [3.5, 3.6, 3.7, 3.8] + python-version: 3.6 steps: - uses: actions/checkout@v1 @@ -65,7 +65,7 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install -r requirements_strict.txt + pip install -r .github/requirements_strict.txt pip install flake8 pytest "pytest-cov<2.6" codecov pip install -U "sklearn" - name: Lint with flake8 From c19d9d3b100f22ee08bd0fa6c879f8f90466081d Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Sun, 3 May 2020 14:31:58 +0200 Subject: [PATCH 07/21] (yet another) bugfix in minimal deps build --- .github/workflows/pythonpackage.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 5ed06e4fb..948ab8b0e 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -54,7 +54,7 @@ jobs: strategy: max-parallel: 4 matrix: - python-version: 3.6 + python-version: [3.6] steps: - uses: actions/checkout@v1 From d782a0110186d83cbd8d61d3e634448b168deb64 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Sun, 3 May 2020 14:57:33 +0200 Subject: [PATCH 08/21] minimal deps now reflect README.md --- .github/requirements_strict.txt | 8 ++++---- README.md | 2 +- setup.py | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/requirements_strict.txt b/.github/requirements_strict.txt index 43ca36814..13cf7c353 100644 --- a/.github/requirements_strict.txt +++ b/.github/requirements_strict.txt @@ -1,7 +1,7 @@ -numpy -scipy==1.2.* -cython -matplotlib +numpy==1.11.* +scipy==1.0.* +cython==0.23.* +matplotlib==1.5.* autograd pymanopt==0.2.4; python_version <'3' pymanopt; python_version >= '3' diff --git a/README.md b/README.md index 51fc02273..b9b8f4576 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ year={2017} The library has been tested on Linux, MacOSX and Windows. It requires a C++ compiler for building/installing the EMD solver and relies on the following Python modules: - Numpy (>=1.11) -- Scipy (>=1.3) +- Scipy (>=1.0) - Cython (>=0.23) - Matplotlib (>=1.5) diff --git a/setup.py b/setup.py index 3f658923a..4640d00c1 100755 --- a/setup.py +++ b/setup.py @@ -67,7 +67,7 @@ scripts=[], data_files=[], requires=["numpy", "scipy", "cython"], - install_requires=["numpy", "scipy>=1.3", "cython"], + install_requires=["numpy", "scipy", "cython"], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Developers', From 2ec2dfb42a6d3dc114cbad4783e6b68ef9455b6b Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 08:34:04 +0200 Subject: [PATCH 09/21] minimal deps: no autograd nor pymanopt --- .github/requirements_strict.txt | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/requirements_strict.txt b/.github/requirements_strict.txt index 13cf7c353..36cbe0264 100644 --- a/.github/requirements_strict.txt +++ b/.github/requirements_strict.txt @@ -1,10 +1,7 @@ numpy==1.11.* scipy==1.0.* cython==0.23.* -matplotlib==1.5.* -autograd -pymanopt==0.2.4; python_version <'3' -pymanopt; python_version >= '3' +matplotlib cvxopt scikit-learn pytest From 0a742a777d1c18bccc210c2fb55da46ad4a921ce Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 08:40:59 +0200 Subject: [PATCH 10/21] refactored workflow names --- .github/workflows/main.yml | 13 --- .github/workflows/pythonpackage.yml | 139 ---------------------------- 2 files changed, 152 deletions(-) delete mode 100644 .github/workflows/main.yml delete mode 100644 .github/workflows/pythonpackage.yml diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml deleted file mode 100644 index ae7bfcad6..000000000 --- a/.github/workflows/main.yml +++ /dev/null @@ -1,13 +0,0 @@ -name: circleci-redirector -on: [status] -jobs: - circleci_artifacts_redirector_job: - runs-on: ubuntu-latest - name: Run CircleCI artifacts redirector - steps: - - name: GitHub Action step - uses: larsoner/circleci-artifacts-redirector-action@master - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} - artifact-path: 0/dev/index.html - circleci-jobs: build_docs diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml deleted file mode 100644 index 948ab8b0e..000000000 --- a/.github/workflows/pythonpackage.yml +++ /dev/null @@ -1,139 +0,0 @@ -name: build - -on: - push: - branches: - - '**' - create: - branches: - - 'master' - tags: - - '**' - -jobs: - linux: - - runs-on: ubuntu-latest - strategy: - max-parallel: 4 - matrix: - python-version: [3.5, 3.6, 3.7, 3.8] - - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - pip install flake8 pytest "pytest-cov<2.6" codecov - pip install -U "sklearn" - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot - - name: Upload codecov - run: | - codecov - - - linux-minimal-deps: - - runs-on: ubuntu-latest - strategy: - max-parallel: 4 - matrix: - python-version: [3.6] - - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r .github/requirements_strict.txt - pip install flake8 pytest "pytest-cov<2.6" codecov - pip install -U "sklearn" - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot - - name: Upload codecov - run: | - codecov - - - macos: - runs-on: macOS-latest - strategy: - max-parallel: 4 - matrix: - python-version: [3.7] - - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - pip install pytest "pytest-cov<2.6" - pip install -U "sklearn" - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot - - - windows: - runs-on: windows-2019 - strategy: - max-parallel: 4 - matrix: - python-version: [3.7] - - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - pip install pytest "pytest-cov<2.6" - pip install -U "sklearn" - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot From 2eedb71438289a4a1f65d6a6e493a41be79afb3b Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 08:45:42 +0200 Subject: [PATCH 11/21] minimal deps: no doctests --- .github/workflows/build_test.yml | 134 ++++++++++++++++++++++ .github/workflows/circleci-redirector.yml | 13 +++ 2 files changed, 147 insertions(+) create mode 100644 .github/workflows/build_test.yml create mode 100644 .github/workflows/circleci-redirector.yml diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml new file mode 100644 index 000000000..8d20ee623 --- /dev/null +++ b/.github/workflows/build_test.yml @@ -0,0 +1,134 @@ +name: build + +on: + push: + create: + branches: + - 'master' + tags: + - '**' + +jobs: + linux: + + runs-on: ubuntu-latest + strategy: + max-parallel: 4 + matrix: + python-version: [3.5, 3.6, 3.7, 3.8] + + steps: + - uses: actions/checkout@v1 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r requirements.txt + pip install flake8 pytest "pytest-cov<2.6" codecov + pip install -U "sklearn" + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics + - name: Install POT + run: | + pip install -e . + - name: Run tests + run: | + python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot + - name: Upload codecov + run: | + codecov + + + linux-minimal-deps: + + runs-on: ubuntu-latest + strategy: + max-parallel: 4 + matrix: + python-version: [3.6] + + steps: + - uses: actions/checkout@v1 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r .github/requirements_strict.txt + pip install flake8 pytest "pytest-cov<2.6" codecov + pip install -U "sklearn" + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics + - name: Install POT + run: | + pip install -e . + - name: Run tests + run: | + python -m pytest -v test/ ot/ --ignore ot/gpu/ + + + macos: + runs-on: macOS-latest + strategy: + max-parallel: 4 + matrix: + python-version: [3.7] + + steps: + - uses: actions/checkout@v1 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r requirements.txt + pip install pytest "pytest-cov<2.6" + pip install -U "sklearn" + - name: Install POT + run: | + pip install -e . + - name: Run tests + run: | + python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot + + + windows: + runs-on: windows-2019 + strategy: + max-parallel: 4 + matrix: + python-version: [3.7] + + steps: + - uses: actions/checkout@v1 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r requirements.txt + pip install pytest "pytest-cov<2.6" + pip install -U "sklearn" + - name: Install POT + run: | + pip install -e . + - name: Run tests + run: | + python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot diff --git a/.github/workflows/circleci-redirector.yml b/.github/workflows/circleci-redirector.yml new file mode 100644 index 000000000..ae7bfcad6 --- /dev/null +++ b/.github/workflows/circleci-redirector.yml @@ -0,0 +1,13 @@ +name: circleci-redirector +on: [status] +jobs: + circleci_artifacts_redirector_job: + runs-on: ubuntu-latest + name: Run CircleCI artifacts redirector + steps: + - name: GitHub Action step + uses: larsoner/circleci-artifacts-redirector-action@master + with: + repo-token: ${{ secrets.GITHUB_TOKEN }} + artifact-path: 0/dev/index.html + circleci-jobs: build_docs From 5dbdbbdfaedde37681ae78a875a5a856fb41efe2 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:08:17 +0200 Subject: [PATCH 12/21] minimal deps: numpy 1.16 --- .github/requirements_strict.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/requirements_strict.txt b/.github/requirements_strict.txt index 36cbe0264..d7539c50e 100644 --- a/.github/requirements_strict.txt +++ b/.github/requirements_strict.txt @@ -1,4 +1,4 @@ -numpy==1.11.* +numpy==1.16.* scipy==1.0.* cython==0.23.* matplotlib From 1893fc2ee3bd4897da682e010f8f5a65a3d3a296 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:09:25 +0200 Subject: [PATCH 13/21] trigger GH Actions on PR --- .github/workflows/build_test.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml index 8d20ee623..601756cb5 100644 --- a/.github/workflows/build_test.yml +++ b/.github/workflows/build_test.yml @@ -2,6 +2,9 @@ name: build on: push: + + pull_request: + create: branches: - 'master' From 5a105974597278d593e9b750ae80c8b30a2980d9 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:10:52 +0200 Subject: [PATCH 14/21] better merge --- .github/workflows/build_test.yml | 137 ------------------------------ .github/workflows/build_tests.yml | 4 +- 2 files changed, 2 insertions(+), 139 deletions(-) delete mode 100644 .github/workflows/build_test.yml diff --git a/.github/workflows/build_test.yml b/.github/workflows/build_test.yml deleted file mode 100644 index 601756cb5..000000000 --- a/.github/workflows/build_test.yml +++ /dev/null @@ -1,137 +0,0 @@ -name: build - -on: - push: - - pull_request: - - create: - branches: - - 'master' - tags: - - '**' - -jobs: - linux: - - runs-on: ubuntu-latest - strategy: - max-parallel: 4 - matrix: - python-version: [3.5, 3.6, 3.7, 3.8] - - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - pip install flake8 pytest "pytest-cov<2.6" codecov - pip install -U "sklearn" - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot - - name: Upload codecov - run: | - codecov - - - linux-minimal-deps: - - runs-on: ubuntu-latest - strategy: - max-parallel: 4 - matrix: - python-version: [3.6] - - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r .github/requirements_strict.txt - pip install flake8 pytest "pytest-cov<2.6" codecov - pip install -U "sklearn" - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --ignore ot/gpu/ - - - macos: - runs-on: macOS-latest - strategy: - max-parallel: 4 - matrix: - python-version: [3.7] - - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - pip install pytest "pytest-cov<2.6" - pip install -U "sklearn" - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot - - - windows: - runs-on: windows-2019 - strategy: - max-parallel: 4 - matrix: - python-version: [3.7] - - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r requirements.txt - pip install pytest "pytest-cov<2.6" - pip install -U "sklearn" - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --doctest-modules --ignore ot/gpu/ --cov=ot diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml index 652655f56..0864006de 100644 --- a/.github/workflows/build_tests.yml +++ b/.github/workflows/build_tests.yml @@ -2,9 +2,9 @@ name: build on: push: - branches: - - '**' + pull_request: + create: branches: - 'master' From b758c8c03bcd48cd8d7729db7bd3e94d65fd4945 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:19:22 +0200 Subject: [PATCH 15/21] re-add minimal-deps... --- .github/workflows/build_tests.yml | 34 +++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml index 0864006de..7cf246466 100644 --- a/.github/workflows/build_tests.yml +++ b/.github/workflows/build_tests.yml @@ -49,6 +49,40 @@ jobs: codecov + linux-minimal-deps: + + runs-on: ubuntu-latest + strategy: + max-parallel: 4 + matrix: + python-version: [3.6] + + steps: + - uses: actions/checkout@v1 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r .github/requirements_strict.txt + pip install flake8 pytest "pytest-cov<2.6" codecov + pip install -U "sklearn" + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics + - name: Install POT + run: | + pip install -e . + - name: Run tests + run: | + python -m pytest -v test/ ot/ --ignore ot/gpu/ + + macos: runs-on: macOS-latest strategy: From a3d800b06305ad37802ea5e88b331eea5ea3c341 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:22:10 +0200 Subject: [PATCH 16/21] bugfix in yaml --- .github/workflows/build_tests.yml | 60 +++++++++++++++---------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml index 7cf246466..601756cb5 100644 --- a/.github/workflows/build_tests.yml +++ b/.github/workflows/build_tests.yml @@ -49,38 +49,38 @@ jobs: codecov - linux-minimal-deps: + linux-minimal-deps: - runs-on: ubuntu-latest - strategy: - max-parallel: 4 - matrix: - python-version: [3.6] + runs-on: ubuntu-latest + strategy: + max-parallel: 4 + matrix: + python-version: [3.6] - steps: - - uses: actions/checkout@v1 - - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v1 - with: - python-version: ${{ matrix.python-version }} - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install -r .github/requirements_strict.txt - pip install flake8 pytest "pytest-cov<2.6" codecov - pip install -U "sklearn" - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics - - name: Install POT - run: | - pip install -e . - - name: Run tests - run: | - python -m pytest -v test/ ot/ --ignore ot/gpu/ + steps: + - uses: actions/checkout@v1 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v1 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install -r .github/requirements_strict.txt + pip install flake8 pytest "pytest-cov<2.6" codecov + pip install -U "sklearn" + - name: Lint with flake8 + run: | + # stop the build if there are Python syntax errors or undefined names + flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics + # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide + flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics + - name: Install POT + run: | + pip install -e . + - name: Run tests + run: | + python -m pytest -v test/ ot/ --ignore ot/gpu/ macos: From c5766f9a65c2573492186eeaf756acc8ba99d427 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:27:57 +0200 Subject: [PATCH 17/21] enforce np>=1.16 --- .github/workflows/build_tests.yml | 8 +------- README.md | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 9 deletions(-) diff --git a/.github/workflows/build_tests.yml b/.github/workflows/build_tests.yml index 601756cb5..41b08b3ac 100644 --- a/.github/workflows/build_tests.yml +++ b/.github/workflows/build_tests.yml @@ -67,14 +67,8 @@ jobs: run: | python -m pip install --upgrade pip pip install -r .github/requirements_strict.txt - pip install flake8 pytest "pytest-cov<2.6" codecov + pip install pytest pip install -U "sklearn" - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 examples/ ot/ test/ --count --max-line-length=127 --statistics - name: Install POT run: | pip install -e . diff --git a/README.md b/README.md index b9b8f4576..5ee4cee82 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ year={2017} The library has been tested on Linux, MacOSX and Windows. It requires a C++ compiler for building/installing the EMD solver and relies on the following Python modules: -- Numpy (>=1.11) +- Numpy (>=1.16) - Scipy (>=1.0) - Cython (>=0.23) - Matplotlib (>=1.5) diff --git a/setup.py b/setup.py index 4640d00c1..bcaa68f45 100755 --- a/setup.py +++ b/setup.py @@ -67,7 +67,7 @@ scripts=[], data_files=[], requires=["numpy", "scipy", "cython"], - install_requires=["numpy", "scipy", "cython"], + install_requires=["numpy>=1.16", "scipy", "cython"], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Developers', From 9ae1208721f98471511b37aadb6ffc254159558d Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:31:03 +0200 Subject: [PATCH 18/21] enforce scipy and cython versions too --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index bcaa68f45..7679c85b6 100755 --- a/setup.py +++ b/setup.py @@ -67,7 +67,7 @@ scripts=[], data_files=[], requires=["numpy", "scipy", "cython"], - install_requires=["numpy>=1.16", "scipy", "cython"], + install_requires=["numpy>=1.16", "scipy>=1.0", "cython>=0.23"], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Developers', From 1916b078f26a857a02556cd2138a946c9e13b8a4 Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:31:51 +0200 Subject: [PATCH 19/21] requires / install_requires --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 7679c85b6..a57a200c9 100755 --- a/setup.py +++ b/setup.py @@ -66,8 +66,8 @@ license='MIT', scripts=[], data_files=[], - requires=["numpy", "scipy", "cython"], - install_requires=["numpy>=1.16", "scipy>=1.0", "cython>=0.23"], + requires=["numpy>=1.16", "scipy>=1.0", "cython>=0.23"], + install_requires=["numpy", "scipy", "cython"], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Developers', From 5e7702e430e9c27f8be93b6b4e1fe2909622d3db Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:37:12 +0200 Subject: [PATCH 20/21] requires / install_requires / requires --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index a57a200c9..7679c85b6 100755 --- a/setup.py +++ b/setup.py @@ -66,8 +66,8 @@ license='MIT', scripts=[], data_files=[], - requires=["numpy>=1.16", "scipy>=1.0", "cython>=0.23"], - install_requires=["numpy", "scipy", "cython"], + requires=["numpy", "scipy", "cython"], + install_requires=["numpy>=1.16", "scipy>=1.0", "cython>=0.23"], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Intended Audience :: Developers', From 4f66436f1a65b3c16b13a008c7c79946f463929d Mon Sep 17 00:00:00 2001 From: Romain Tavenard Date: Mon, 4 May 2020 10:43:39 +0200 Subject: [PATCH 21/21] setup_requires --- setup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/setup.py b/setup.py index 7679c85b6..91c24d911 100755 --- a/setup.py +++ b/setup.py @@ -67,6 +67,7 @@ scripts=[], data_files=[], requires=["numpy", "scipy", "cython"], + setup_requires=["numpy>=1.16", "scipy>=1.0", "cython>=0.23"], install_requires=["numpy>=1.16", "scipy>=1.0", "cython>=0.23"], classifiers=[ 'Development Status :: 5 - Production/Stable',