tofu 1.4.2 preparation

.travis.yml

@@ -1,69 +1,127 @@
 language: python
-python:
-- '3.6'
-- '3.7-dev'
-
-git:
-  depth: 200
-sudo: required
-dist: trusty
+matrix:
+  include:
+  - name: Bionic python 3.7
+    os: linux
+    dist: bionic
+    python: 3.7
+    env:
+    - REPO=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    - OS=linux-64
+  - name: trusty python 3.6
+    os: linux
+    dist: trusty
+    python: 3.6
+    env:
+    - REPO=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    - OS=linux-64
+  - name: xenial python 3.7
+    os: linux
+    dist: xenial
+    python: 3.7
+    env:
+    - REPO=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    - OS=linux-64
+  - name: xenial python 3.6
+    os: linux
+    dist: xenial
+    python: 3.6
+    env:
+    - REPO=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+    - OS=linux-64
+  - name: osx python 3.7
+    os: osx
+    language: generic
+    env:
+    - REPO=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+    - TRAVIS_PYTHON_VERSION=3.7
+    - OS=osx-64
+  - name: osx python 3.6
+    os: osx
+    language: generic
+    env:
+    - REPO=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
+    - TRAVIS_PYTHON_VERSION=3.6
+    - OS=osx-64
 before_install:
-  - sudo apt-get update
-  - ldd --version
-  - gcc --version
-  - export START=$(pwd)
+- gcc --version
+- export START=$(pwd)
 install:
-- if [[ "$TRAVIS_PYTHON_VERSION" == "3.7-dev" ]]; then export VADD="py37"; else export VADD="py36";  fi
-- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-  -O miniconda.sh
+- wget "$REPO" -O miniconda.sh
 - bash miniconda.sh -b -p $HOME/miniconda
 - export PATH="$HOME/miniconda/bin:$PATH"
 - hash -r
 - conda config --set always_yes yes --set changeps1 no
-- conda install conda-build
-- conda update -q conda
-- conda update -n root conda-build
-- conda config --set anaconda_upload no
 - conda config --append channels conda-forge
 - conda config --append channels tofuproject
 - conda info -a
-- if [[ "$TRAVIS_PYTHON_VERSION" == "3.7-dev" ]]; then export THIS_PY_VERSION="3.7";
-  else THIS_PY_VERSION=$TRAVIS_PYTHON_VERSION;
-  fi
-- conda install -q python=$THIS_PY_VERSION conda-build anaconda-client nose
-  nose-timer coverage codecov
+- conda install -q python="$TRAVIS_PYTHON_VERSION" conda-verify nose nose-timer coverage
+  codecov
 - export REV=$(python -c "import _updateversion as up; out=up.updateversion(); print(out)")
 - export VERSION=$(echo $REV | tr - .)
 - echo $REV
-- conda build conda_recipe
-- export PKG_DIR=$HOME/miniconda/conda-bld/linux-64/
-- conda install tofu --use-local
+- pip install -e ".[dev]"
 script:
 - cd $HOME
-- nosetests tofu.tests --nocapture -v --with-id --with-timer --with-coverage
-  --cover-package=tofu
+- nosetests tofu.tests --nocapture -v --with-id --with-timer --with-coverage --cover-package=tofu
 after_success:
 - codecov
 - chmod +x $START/anaconda_upload.sh
 - echo $TRAVIS_TAG
 before_deploy:
+- echo "BEFORE DEPLOY START........"
 - ls $START
 - cd $START
+- conda config --set anaconda_upload no
+- conda install anaconda-client conda-build
+- conda build conda_recipe
+- export PKG_REAL=$(conda build . --output | tail -1)
+- echo "BEFORE DEPLOY END.........."
 deploy:
-  - provider: script
-    user: "ToFuProject"
-    script: $START/anaconda_upload.sh
+  - provider: pypi
+    distributions: sdist
+    user: __token__
+    skip_existing: true
     on:
       tags: true
-      all_branches: true
-    skip_cleanup: true
+      branch: deploy-test
+    server: https://test.pypi.org/legacy/
+    password:
+      secure: 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
+  - provider: pypi
+    distributions: bdist_wheel
+    user: __token__
+    skip_existing: true
+    on:
+      condition: $OS = osx-64
+      tags: true
+      branch: deploy-test
+    server: https://test.pypi.org/legacy/
+    password:
+      secure: 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
   - provider: pypi
+    distributions: sdist
     user: "Didou09"
-    distributions: "sdist"
-    skip_cleanup: true
     skip_existing: true
     on:
       tags: true
-      all_branches: true
+      branch: master
     password:
       secure: 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
+  - provider: pypi
+    distributions: bdist_wheel
+    user: "Didou09"
+    skip_existing: true
+    on:
+      condition: $OS = osx-64
+      tags: true
+      branch: master
+    password:
+      secure: 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
+  - provider: script
+    user: "ToFuProject"
+    script: $START/anaconda_upload.sh
+    on:
+      tags: true
+      branch: master
+    skip_cleanup: true

Notebooks/Cython_speedup_notes.ipynb

@@ -94,20 +94,20 @@
      "output_type": "stream",
      "text": [
       "For L =  1000\n",
-      "0.360000 μs, using the untyped_func\n",
-      "0.123000 μs, using the somewhat_typed_func\n",
-      "0.113000 μs, using the typed_func\n",
-      "0.029000 μs, using the inline_typed_func\n",
+      "0.798000 μs, using the untyped_func\n",
+      "0.027000 μs, using the somewhat_typed_func\n",
+      "0.017000 μs, using the typed_func\n",
+      "0.008000 μs, using the inline_typed_func\n",
       "For L =  10000\n",
-      "5.174000 μs, using the untyped_func\n",
-      "0.024000 μs, using the somewhat_typed_func\n",
-      "0.012000 μs, using the typed_func\n",
-      "0.015000 μs, using the inline_typed_func\n",
+      "8.871000 μs, using the untyped_func\n",
+      "0.027000 μs, using the somewhat_typed_func\n",
+      "0.014000 μs, using the typed_func\n",
+      "0.014000 μs, using the inline_typed_func\n",
       "For L =  100000\n",
-      "43.197000 μs, using the untyped_func\n",
-      "0.151000 μs, using the somewhat_typed_func\n",
-      "0.025000 μs, using the typed_func\n",
-      "0.024000 μs, using the inline_typed_func\n"
+      "81.221000 μs, using the untyped_func\n",
+      "0.148000 μs, using the somewhat_typed_func\n",
+      "0.010000 μs, using the typed_func\n",
+      "0.015000 μs, using the inline_typed_func\n"
      ]
     }
    ],
@@ -200,7 +200,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -210,19 +210,19 @@
       "\n",
       "-------- TESTS -------\n",
       "Running numpy buffers\n",
-      "0.020667 0.009333 0.098333 0.882333 6.571667 58.261333 670.627333 μs\n",
+      "0.010667 0.027000 0.108667 0.926667 11.027667 95.586333 1118.653333 μs\n",
       "Running cpython.array buffer\n",
-      "0.327333 0.090000 0.323333 0.742333 7.339333 70.054000 1853.809000 μs\n",
+      "0.074667 0.091667 0.351667 3.606667 25.803333 230.891000 2605.097000 μs\n",
       "Running cpython.array memoryview\n",
-      "0.890333 0.785000 1.215667 1.305667 6.270667 44.810333 538.815667 μs\n",
+      "0.325333 0.398667 1.079000 1.887667 7.430000 79.003667 1005.866000 μs\n",
       "Running cpython.array raw C type with trick\n",
-      "0.044000 0.048667 0.380000 1.419333 10.037000 100.486667 2541.475333 μs\n",
+      "0.035000 0.041667 0.119667 0.787667 8.991000 93.519667 1401.235667 μs\n",
       "Running C pointers\n",
-      "0.006000 0.006333 0.023667 0.159000 2.129667 25.866667 363.967667 μs\n",
+      "0.005000 0.006667 0.057333 0.563333 5.081000 35.753000 887.650667 μs\n",
       "Running malloc memoryview\n",
-      "0.588667 0.630333 0.663667 1.224333 2.392333 23.987667 379.138667 μs\n",
+      "0.482333 1.043333 0.778000 1.127333 6.685000 53.277667 798.593333 μs\n",
       "Running argument memoryview\n",
-      "0.011667 0.016333 0.112000 0.722667 5.305000 45.683333 525.975333 μs\n"
+      "0.008000 0.019000 0.156000 1.217000 10.740000 96.713667 1305.644333 μs\n"
      ]
     }
    ],
@@ -391,7 +391,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -402,9 +402,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 6,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "For L =  1000\n",
+      "10.211000 μs, using the sequential loop\n",
+      "58.846000 μs, using the parallel 1 loop\n",
+      "25.343000 μs, using the parallel 2 loop\n",
+      "For L =  10000\n",
+      "53.134000 μs, using the sequential loop\n",
+      "180.918000 μs, using the parallel 1 loop\n",
+      "49.014000 μs, using the parallel 2 loop\n",
+      "For L =  100000\n",
+      "827.005000 μs, using the sequential loop\n",
+      "601.007000 μs, using the parallel 1 loop\n",
+      "132.242000 μs, using the parallel 2 loop\n"
+     ]
+    }
+   ],
    "source": [
     "%%cython --compile=-fopenmp --link-args=-fopenmp\n",
     "\n",
@@ -650,7 +669,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.2"
+   "version": "3.7.5"
   }
  },
  "nbformat": 4,