Merge branch 'master' of https://github.com/sdpython/mlinsights into dev

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2
 jobs:
   build:
     docker:
-      - image: circleci/python:3.7.5
+      - image: circleci/python:3.9.1
 
     working_directory: ~/repo
 
@@ -11,15 +11,15 @@ jobs:
 
       - restore_cache:
           keys:
-          - v3-dependencies-{{ checksum "requirements.txt" }}
-          - v3-dependencies-
+          - v2-dependencies-{{ checksum "requirements.txt" }}
+          - v2-dependencies-
 
       - run:
           name: Install pandoc
           command: |
                     sudo apt-get update 
-                    wget https://github.com/jgm/pandoc/releases/download/2.2.1/pandoc-2.2.1-1-amd64.deb
-                    sudo dpkg -i pandoc-2.2.1-1-amd64.deb
+                    wget https://github.com/jgm/pandoc/releases/download/2.11.3.2/pandoc-2.11.3.2-1-amd64.deb
+                    sudo dpkg -i pandoc-2.11.3.2-1-amd64.deb
           
       - run:
           name: Install tex
@@ -43,53 +43,71 @@ jobs:
           command: |
                     sudo apt-get install -y graphviz
           
-      # statsmodels setup.py requires it
       - run:
-          name: install numpy
+          name: Install libproj
           command: |
-            python3 -m venv venv
+            sudo apt-get install -y libgeos-dev libproj-dev proj-data graphviz
+
+      - run:
+          name: Install llvmlite
+          command: |
+            sudo apt-get install lsb-release wget software-properties-common
+            wget https://apt.llvm.org/llvm.sh
+            chmod +x llvm.sh
+            sudo ./llvm.sh 10
+            ls /usr/bin/llvm*
+
+      - run:
+          name: Install standard libraries
+          command: |
+            python -m venv venv
             . venv/bin/activate
-            pip install numpy
+            pip install scipy matplotlib numpy cython pandas
 
       - run:
-          name: Install cython
+          name: Install pyproj, shapely, cartopy
           command: |
-            python3 -m venv venv
+            python -m venv venv
             . venv/bin/activate
-            pip install cython
+            pip install pyproj
+            pip uninstall -y shapely
+            pip install --no-binary shapely shapely
+            pip install cartopy
 
       - run:
-          name: Install geos, proj for cartopy
+          name: Install numba, llvmlite
           command: |
-            sudo apt-get -qq update
-            sudo apt-get install -y libproj-dev proj-bin proj-data
-            sudo apt-get install -y python-pyproj
-            sudo apt-get install -y libc6
-            sudo apt-get install libgeos-dev
-            sudo apt-get install python-gdal gdal-bin
-            wget http://es.archive.ubuntu.com/ubuntu/pool/universe/p/proj/libproj9_4.9.2-2_amd64.deb 
-            sudo dpkg -i libproj9_4.9.2-2_amd64.deb 
-            wget http://es.archive.ubuntu.com/ubuntu/pool/universe/p/proj/libproj-dev_4.9.2-2_amd64.deb
-            sudo dpkg -i libproj-dev_4.9.2-2_amd64.deb
+            python -m venv venv
+            . venv/bin/activate
+            # export LLVM_CONFIG=/usr/local/opt/llvm/bin/llvm-config
+            sudo ln -s /usr/bin/llvm-config-10 /usr/bin/llvm-config
+            pip install llvmlite numba
 
       - run:
           name: install dependencies
           command: |
-            python3 -m venv venv
+            python -m venv venv
             . venv/bin/activate
-            pip install scipy
             pip install -r requirements.txt
 
       - save_cache:
           paths:
             - ./venv
-          key: v3-dependencies-{{ checksum "requirements.txt" }}
+          key: v2-dependencies-{{ checksum "requirements.txt" }}
+
+      - run:
+          name: check list of dependencies
+          command: |
+            python -m venv venv
+            . venv/bin/activate
+            pip freeze
+            apt list --installed
         
       - run:
           name: compile and build
           command: |
             . venv/bin/activate
-            python -u setup.py build_ext --inplace --verbose
+            python setup.py build_ext --inplace
 
       - run:
           name: run tests
@@ -101,23 +119,23 @@ jobs:
           name: wheel
           command: |
             . venv/bin/activate
-            python ./setup.py bdist_wheel
+            python setup.py bdist_wheel
             mkdir -p test-reports/dist
             cp dist/*.whl test-reports/dist
             mkdir -p test-reports
             cp -r  mlinsights test-reports
 
-      - run:
-          name: documentation
-          command: |
-            . venv/bin/activate
-            python setup.py build_sphinx
-            
-      - run:
-          name: copy documentation
-          command: |
-            mkdir -p test-reports/doc
-            zip -r -9  test-reports/doc/documentation_html.zip _doc/sphinxdoc/build/html
+#      - run:
+#          name: documentation
+#          command: |
+#           . venv/bin/activate
+#           python setup.py build_sphinx
+#           
+#      - run:
+#          name: copy documentation
+#          command: |
+#           mkdir -p test-reports/doc
+#           zip -r -9  test-reports/doc/documentation_html.zip _doc/sphinxdoc/build/html
 
       - store_artifacts:
           path: test-reports

.local.jenkins.lin.yml

@@ -2,8 +2,7 @@
 language: python
 
 python:
-  - { PATH: "{{Python37}}", VERSION: 3.7, DIST: std, PYINT: python3.7 }
-  - { PATH: "{{Python38}}", VERSION: 3.8, DIST: std, PYINT: python3.8 }
+  - { PATH: "{{Python39}}", VERSION: 3.9, DIST: std, PYINT: python3.9 }
 
 virtualenv:
   - path: {{ospathjoin(root_path, pickname("$NAME_JENKINS", project_name + "_$VERSION_$DIST_$NAME"), "_venv")}}
@@ -12,8 +11,8 @@ install:
   - $PYINT -m pip install --upgrade pip
   - $PYINT -m pip install --upgrade --no-cache-dir --no-deps --index http://localhost:8067/simple/ jyquickhelper pyquickhelper cpyquickhelper pandas_streaming --extra-index-url=https://pypi.python.org/simple/
   - $PYINT -m pip install --upgrade --no-cache-dir --no-deps --index http://localhost:8067/simple/ scikit-learn>=0.22 --extra-index-url=https://pypi.python.org/simple/
+  - $PYINT -m pip install -r requirements-win.txt
   - $PYINT -m pip install -r requirements.txt
-  - $PYINT -m pip install -r requirements-ext.txt
   - $PYINT --version
   - $PYINT -m pip freeze
 

.local.jenkins.win.yml

@@ -2,16 +2,14 @@
 language: python
 
 python:
-  - { PATH: "{{replace(Python37, '\\', '\\\\')}}", VERSION: 3.7, DIST: std }
+  - { PATH: "{{replace(Python39, '\\', '\\\\')}}", VERSION: 3.9, DIST: std }
 
 virtualenv:
   - path: {{ospathjoin(root_path, pickname("%NAME_JENKINS%", project_name + "_%VERSION%_%DIST%_%NAME%"), "_venv")}}
 
 install:
   - pip install --upgrade pip
-  - pip install --no-cache-dir --no-deps --index http://localhost:8067/simple/ jyquickhelper --extra-index-url=https://pypi.python.org/simple/
-  - pip install --no-cache-dir --no-deps --index http://localhost:8067/simple/ pyquickhelper --extra-index-url=https://pypi.python.org/simple/
-  - pip install --no-cache-dir --no-deps --index http://localhost:8067/simple/ cpyquickhelper --extra-index-url=https://pypi.python.org/simple/
+  - pip install --no-cache-dir --no-deps --index http://localhost:8067/simple/ jyquickhelper pyquickhelper cpyquickhelper --extra-index-url=https://pypi.python.org/simple/
   - pip install -r requirements.txt
   - pip freeze
   - pip freeze > pip_freeze.txt

.travis.yml

@@ -1,27 +1,37 @@
-dist: bionic
+dist: focal
 sudo: true
 language: python
 
 matrix:
   include:
-  - python: 3.7
-    name: "Py37-skl022"
-    env: sklearnc="==0.22.2"
+  - python: 3.9
+    name: "Py39-024+"
+    env:
+      - sklver=">=0.24.0"
+      - jlver=">=1.0"
   - python: 3.8
-    name: "Py38-skl023"
-    env: sklearnc=">=0.23"
+    name: "Py38-023"
+    env:
+      - sklver="==0.23.2"
+      - jlver="==0.17.0"
+
 before_install:
-  - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
-  - sudo apt-get update -qq
-  - sudo apt-get install graphviz
-  - gcc --version
+    - sudo apt-get install libgeos-dev libproj-dev proj-data graphviz libblas-dev liblapack-dev
+    - wget https://apt.llvm.org/llvm.sh
+    - chmod +x llvm.sh
+    - sudo ./llvm.sh 10
+    - ls /usr/bin/llvm*
+    - export LLVM_CONFIG=/usr/bin/llvm-config
+    # - sudo ln -s /usr/bin/llvm-config-10 /usr/bin/llvm-config
+    - sudo apt-get -y install graphviz      
+
 install:
-  - pip install pyquickhelper cython scipy
   - pip install -r requirements.txt
-  - pip install -r requirements-ext.txt
-  - pip install scikit-learn$sklearnc
-  - python -c "import sklearn;print(sklearn.__version__)"
+  - pip install "scikit-learn$sklver"
+  - pip install "joblib$jlver"
+
 before_script:
-  - python -u setup.py build_ext --inplace --verbose
+  - python setup.py build_ext --inplace
+
 script:
   - python setup.py unittests

HISTORY.rst

@@ -5,11 +5,34 @@
 History
 =======
 
-current - 2020-08-06 - 0.00Mb
+current - 2021-01-09 - 0.00Mb
 =============================
 
-* `81`: Make mlinsights work with scikit-learn 0.22 and 0.23 (2020-08-06)
+* `93`: Include build wheel for all platforms in CI (2021-01-09)
+
+0.3.543 - 2021-01-03 - 0.67Mb
+=============================
+
+* `89`: Install fails: ModuleNotFoundError: No module named 'sklearn' (2021-01-03)
+* `92`: QuantileMLPRegressor does not work with scikit-learn 0.24 (2021-01-01)
+* `91`: Fixes regression criterion for scikit-learn 0.24 (2021-01-01)
+* `90`: Fixes PipelineCache for scikit-learn 0.24 (2021-01-01)
+
+0.2.508 - 2020-09-02 - 0.43Mb
+=============================
+
+* `88`: Change for scikit-learn 0.24 (2020-09-02)
+* `87`: Set up CI with Azure Pipelines (2020-09-02)
+* `86`: Update CI, use python 3.8 (2020-09-02)
+* `71`: update kmeans l1 to the latest kmeans (signatures changed) (2020-08-31)
+* `84`: style (2020-08-30)
+
+0.2.491 - 2020-08-06 - 0.83Mb
+=============================
+
+* `83`: Upgrade version (2020-08-06)
 * `82`: Fixes #81, skl 0.22, 0.23 together (2020-08-06)
+* `81`: Make mlinsights work with scikit-learn 0.22 and 0.23 (2020-08-06)
 * `79`: pipeline2dot fails with 'passthrough' (2020-07-16)
 
 0.2.463 - 2020-06-29 - 0.83Mb

LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2017-2020, Xavier Dupré
+Copyright (c) 2017-2021, Xavier Dupré
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.rst

@@ -18,7 +18,7 @@ mlinsights - extensions to scikit-learn
 .. image:: https://circleci.com/gh/sdpython/mlinsights/tree/master.svg?style=svg
     :target: https://circleci.com/gh/sdpython/mlinsights/tree/master
 
-.. image:: https://dev.azure.com/xavierdupre3/mlinsights/_apis/build/status/sdpython.mlinsights
+.. image:: https://dev.azure.com/xavierdupre3/mlinsights/_apis/build/status/sdpython.mlinsights%20(2)
     :target: https://dev.azure.com/xavierdupre3/mlinsights/
 
 .. image:: https://badge.fury.io/py/mlinsights.svg

_doc/examples/plot_constraint_kmeans.py

@@ -14,21 +14,23 @@
 ====
 """
 from collections import Counter
+import numpy
 import matplotlib.pyplot as plt
 from sklearn.datasets import make_blobs
 from sklearn.cluster import KMeans
 from mlinsights.mlmodel import ConstraintKMeans
 
 
 n_samples = 100
-data = make_blobs(n_samples=n_samples, n_features=2, centers=2, cluster_std=1.0,
-                  center_box=(-10.0, 0.0), shuffle=True, random_state=2)
+data = make_blobs(
+    n_samples=n_samples, n_features=2, centers=2, cluster_std=1.0,
+    center_box=(-10.0, 0.0), shuffle=True, random_state=2)
 X1 = data[0]
-data = make_blobs(n_samples=n_samples // 2, n_features=2, centers=2, cluster_std=1.0,
-                  center_box=(0.0, 10.0), shuffle=True, random_state=2)
+data = make_blobs(
+    n_samples=n_samples // 2, n_features=2, centers=2, cluster_std=1.0,
+    center_box=(0.0, 10.0), shuffle=True, random_state=2)
 X2 = data[0]
 
-import numpy
 X = numpy.vstack([X1, X2])
 X.shape
 

_doc/sphinxdoc/source/blog/2018/2018-05-07_quantile_regression.rst

@@ -10,7 +10,7 @@
     `QuantReg <http://www.statsmodels.org/dev/generated/statsmodels.regression.quantile_regression.QuantReg.html>`_
     but I wanted to try something I did for my teachings
     `Régression Quantile
-    <http://www.xavierdupre.fr/app/ensae_teaching_cs/helpsphinx3/notebooks/td_note_2017_2.html?highlight=mediane>`_
+    <http://www.xavierdupre.fr/app/ensae_teaching_cs/helpsphinx/notebooks/td_note_2017_2.html?highlight=mediane>`_
     based on `Iteratively reweighted least squares
     <https://en.wikipedia.org/wiki/Iteratively_reweighted_least_squares>`_.
     I thought it was a good case study to turn a simple algorithm into

_doc/sphinxdoc/source/blog/2020/2020-09-02_api.rst

@@ -0,0 +1,22 @@
+
+.. blogpost::
+    :title: scikit-learn internal API
+    :keywords: API
+    :date: 2020-09-02
+    :categories: scikit-learn
+    :lid: blog-internal-api-impurity-improvement
+
+    The signature of method `impurity_improvement
+    <https://github.com/scikit-learn/scikit-learn/blob/master/
+    sklearn/tree/_criterion.pxd#L65>`_ will change for version
+    0.24. That's usually easy to handle two versions of scikit-learn
+    even overloaded in a class except that method is implemented
+    in :epkg:`cython`. The method must be overloaded the same way
+    with the same signature. The way it was handled is implemented
+    in PR `88 <https://github.com/sdpython/mlinsights/pull/88>`_.
+
+    The best would be to include both of them but only one of
+    them can compile. I did not find any good solution to that.
+    It compiles whatever scikit-learn's version but the compiled
+    module only works with the installed version of
+    :epkg:`scikti-learn`.

_doc/sphinxdoc/source/blog/2021/2021-01-03_skl.rst

@@ -0,0 +1,15 @@
+
+.. blogpost::
+    :title: scikit-learn 0.23
+    :keywords: scikit-learn, 0.23, 0.24
+    :date: 2021-01-03
+    :categories: scikit-learn
+
+    The unit test are run against
+    :epkg:`scikit-learn` 0.23, 0.24.
+    Some unit tests are failing with version 0.23.
+    They were disabled instead of looking into a cause
+    which does not appear with the latest version.
+    It affects all classes inheriting from :class:`SkBase
+    <mlinsights.sklapi.sklearn_base.SkBase>` where a model
+    using it is trained. The issue happens in :epkg:`joblib`.

_doc/sphinxdoc/source/conf.py

@@ -13,7 +13,7 @@
 local_template = os.path.join(os.path.abspath(
     os.path.dirname(__file__)), "phdoc_templates")
 
-set_sphinx_variables(__file__, "mlinsights", "Xavier Dupré", 2020,
+set_sphinx_variables(__file__, "mlinsights", "Xavier Dupré", 2021,
                      "alabaster", alabaster.get_path(),
                      locals(), extlinks=dict(
                          issue=('https://github.com/sdpython/mlinsights/issues/%s', 'issue')),