Merge pull request #18 from bionumpy/dev

Dev

.github/workflows/asv_benchmark.yml

@@ -0,0 +1,66 @@
+name: ASV Benchmarks
+
+on:
+  push:
+    branches: [ "dev"]
+  pull_request:
+    branches: [ "dev" ]
+
+permissions:
+  contents: write
+
+jobs:
+  build:
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.10"
+      - name: Run asv
+        uses: actions/checkout@v3
+      - run: |
+         git config --global user.email "[email protected]"
+         git config --global user.name "github action"
+         git config pull.rebase false
+         # merge in gh-pages to get old results before generating new
+         git fetch
+         git merge origin/gh-pages --strategy-option ours --allow-unrelated-histories
+         python -m pip install --upgrade pip
+         pip install -r requirements_dev.txt
+         pip install .
+      - run: pip install asv
+      - run: asv machine --machine github_actions --yes  # give this machine a name so that all results are linked to the same, hostname changes if not
+      - run: asv run --verbose --machine github_actions  # make sure to use the machine name so that it does not use hostname
+      - run: asv publish --verbose
+
+      - name: Save benchmarks results
+        run: |
+          
+          #git checkout --orphan benchmarks
+          #git fetch
+          # merge in gh-pages to get old results before generating new
+          #git merge origin/gh-pages --strategy-option ours --allow-unrelated-histories
+          
+          mkdir -p docs/asv
+          cp -R .asv/html/* docs/asv/
+          git add -f .asv/results/*
+          git add -f docs/asv/*
+          git commit -am 'Benchmark results'
+          
+          git checkout gh-pages
+          # merge asv branch into gh-pages, keep asv changes
+          git merge --strategy-option theirs dev --allow-unrelated-histories
+          
+          #git pull -s recursive -X ours origin gh-pages
+
+      - name: Push results
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          tags: true
+          force: true
+          branch: gh-pages
+

.github/workflows/build_sphinx_website.yml

@@ -29,12 +29,18 @@ jobs:
       - name: make html & commit the changes
         run: |
           sphinx-build -b html ./docs_source ./docs
-          git config user.name "knutrand"
+          git config user.name "github actions"
+          git config --global user.email "[email protected]"
+          git config pull.rebase false
+          
           git add -f ./docs
           git commit -m 'update docs'
           
+          git pull -s recursive -X ours origin gh-pages  --allow-unrelated-histories
+          
+          
       - name: push changes to gh-pages to show automatically
         uses: ad-m/github-push-action@master
         with:
           branch: gh-pages
-          force: true
+          #force: true

.github/workflows/bumpversion.yml

@@ -2,7 +2,7 @@ name: Bump version
 on:
   workflow_run:
     workflows: [ "Build and test" ]
-    branches: [ master ]
+    branches: [ main ]
     types:
       - completed
 jobs:

.github/workflows/push-to-pypi.yml

@@ -4,7 +4,7 @@ on:
   # only on successful bumpversion
   workflow_run:
     workflows: [ "Bump version" ]
-    branches: [ master ]
+    branches: [ main ]
     types:
       - completed
 

.github/workflows/python-install-and-test.yml

@@ -5,9 +5,9 @@ name: Build and test
 
 on:
   push:
-    branches: [ "master", "dev" ]
+    branches: [ "main", "dev" ]
   pull_request:
-    branches: [ "master", "dev" ]
+    branches: [ "main", "dev" ]
 
 permissions:
   contents: read

README.rst

@@ -32,6 +32,7 @@ As such, familiarity with `numpy` is assumed. The simplest way to construct a `R
     >>> ra = RaggedArray([[1, 2], [4, 1, 3, 7], [9], [8, 7, 3, 4]])
 
 A `RaggedArray` can be indexed much like a `numpy` array::
+
     >>> ra[1]
     array([4, 1, 3, 7])
     >>> ra[1, 3]
@@ -51,6 +52,7 @@ A `RaggedArray` can be indexed much like a `numpy` array::
     RaggedArray([[2, 2], [10, 10, 10, 10], [3], [5, 5, 5, 5]])
 
 `numpy ufuncs` can be applied to `RaggedArray` objects::
+
     >>> ra + 1
     RaggedArray([[2, 3], [5, 2, 4, 8], [10], [9, 8, 4, 5]])
     >>> ra*2
@@ -61,6 +63,7 @@ A `RaggedArray` can be indexed much like a `numpy` array::
     RaggedArray([[-1, -2], [-4, -1, -3, -7], [-9], [-8, -7, -3, -4]])
 
 Some `numpy` functions can be applied to `RaggedArray` objects::
+
     >>> import numpy as np
     >>> ra = RaggedArray([[1, 2], [4, 1, 3, 7], [9], [8, 7, 3, 4]])
     >>> np.concatenate((ra, ra*10))

asv.conf.json

@@ -0,0 +1,198 @@
+{
+    // The version of the config file format.  Do not change, unless
+    // you know what you are doing.
+    "version": 1,
+
+    // The name of the project being benchmarked
+    "project": "project",
+
+    // The project's homepage
+    "project_url": "https://github.com/npstructures",
+
+    // The URL or local path of the source code repository for the
+    // project being benchmarked
+    "repo": "https://github.com/bionumpy/npstructures.git",
+
+    // The Python project's subdirectory in your repo.  If missing or
+    // the empty string, the project is assumed to be located at the root
+    // of the repository.
+    "repo_subdir": ".",
+
+    // Customizable commands for building the project.
+    // See asv.conf.json documentation.
+    // To build the package using pyproject.toml (PEP518), uncomment the following lines
+    // "build_command": [
+    //     "python -m pip install build",
+    //     "python -m build",
+    //     "python -mpip wheel -w {build_cache_dir} {build_dir}"
+    // ],
+    // To build the package using setuptools and a setup.py file, uncomment the following lines
+    //"build_command": [
+    //     "python setup.py build",
+    //     "python -mpip wheel -w {build_cache_dir} {build_dir}"
+    //],
+    "build_command": [
+        "python -m pip install build",
+        "python -m build --wheel -o {build_cache_dir} {build_dir}",
+    ],
+
+    // Customizable commands for installing and uninstalling the project.
+    // See asv.conf.json documentation.
+    // "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"],
+    // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
+
+    // List of branches to benchmark. If not provided, defaults to "main"
+    // (for git) or "default" (for mercurial).
+    "branches": ["dev"], // for git
+    // "branches": ["default"],    // for mercurial
+
+    // The DVCS being used.  If not set, it will be automatically
+    // determined from "repo" by looking at the protocol in the URL
+    // (if remote), or by looking for special directories, such as
+    // ".git" (if local).
+    // "dvcs": "git",
+
+    // The tool to use to create environments.  May be "conda",
+    // "virtualenv", "mamba" (above 3.8)
+    // or other value depending on the plugins in use.
+    // If missing or the empty string, the tool will be automatically
+    // determined by looking for tools on the PATH environment
+    // variable.
+    "environment_type": "virtualenv",
+
+    // timeout in seconds for installing any dependencies in environment
+    // defaults to 10 min
+    //"install_timeout": 600,
+
+    // the base URL to show a commit for the project.
+    "show_commit_url": "http://github.com/bionumpy/npstructures/commit/",
+
+    // The Pythons you'd like to test against.  If not provided, defaults
+    // to the current version of Python used to run `asv`.
+    // "pythons": ["3.8", "3.12"],
+
+    // The list of conda channel names to be searched for benchmark
+    // dependency packages in the specified order
+    // "conda_channels": ["conda-forge", "defaults"],
+
+    // A conda environment file that is used for environment creation.
+    // "conda_environment_file": "environment.yml",
+
+    // The matrix of dependencies to test.  Each key of the "req"
+    // requirements dictionary is the name of a package (in PyPI) and
+    // the values are version numbers.  An empty list or empty string
+    // indicates to just test against the default (latest)
+    // version. null indicates that the package is to not be
+    // installed. If the package to be tested is only available from
+    // PyPi, and the 'environment_type' is conda, then you can preface
+    // the package name by 'pip+', and the package will be installed
+    // via pip (with all the conda available packages installed first,
+    // followed by the pip installed packages).
+    //
+    // The ``@env`` and ``@env_nobuild`` keys contain the matrix of
+    // environment variables to pass to build and benchmark commands.
+    // An environment will be created for every combination of the
+    // cartesian product of the "@env" variables in this matrix.
+    // Variables in "@env_nobuild" will be passed to every environment
+    // during the benchmark phase, but will not trigger creation of
+    // new environments.  A value of ``null`` means that the variable
+    // will not be set for the current combination.
+    //
+    // "matrix": {
+    //     "req": {
+    //         "numpy": ["1.6", "1.7"],
+    //         "six": ["", null],  // test with and without six installed
+    //         "pip+emcee": [""]   // emcee is only available for install with pip.
+    //     },
+    //     "env": {"ENV_VAR_1": ["val1", "val2"]},
+    //     "env_nobuild": {"ENV_VAR_2": ["val3", null]},
+    // },
+
+    // Combinations of libraries/python versions can be excluded/included
+    // from the set to test. Each entry is a dictionary containing additional
+    // key-value pairs to include/exclude.
+    //
+    // An exclude entry excludes entries where all values match. The
+    // values are regexps that should match the whole string.
+    //
+    // An include entry adds an environment. Only the packages listed
+    // are installed. The 'python' key is required. The exclude rules
+    // do not apply to includes.
+    //
+    // In addition to package names, the following keys are available:
+    //
+    // - python
+    //     Python version, as in the *pythons* variable above.
+    // - environment_type
+    //     Environment type, as above.
+    // - sys_platform
+    //     Platform, as in sys.platform. Possible values for the common
+    //     cases: 'linux2', 'win32', 'cygwin', 'darwin'.
+    // - req
+    //     Required packages
+    // - env
+    //     Environment variables
+    // - env_nobuild
+    //     Non-build environment variables
+    //
+    // "exclude": [
+    //     {"python": "3.2", "sys_platform": "win32"}, // skip py3.2 on windows
+    //     {"environment_type": "conda", "req": {"six": null}}, // don't run without six on conda
+    //     {"env": {"ENV_VAR_1": "val2"}}, // skip val2 for ENV_VAR_1
+    // ],
+    //
+    // "include": [
+    //     // additional env for python3.12
+    //     {"python": "3.12", "req": {"numpy": "1.26"}, "env_nobuild": {"FOO": "123"}},
+    //     // additional env if run on windows+conda
+    //     {"platform": "win32", "environment_type": "conda", "python": "3.12", "req": {"libpython": ""}},
+    // ],
+
+    // The directory (relative to the current directory) that benchmarks are
+    // stored in.  If not provided, defaults to "benchmarks"
+    // "benchmark_dir": "benchmarks",
+
+    // The directory (relative to the current directory) to cache the Python
+    // environments in.  If not provided, defaults to "env"
+    "env_dir": ".asv/env",
+
+    // The directory (relative to the current directory) that raw benchmark
+    // results are stored in.  If not provided, defaults to "results".
+    "results_dir": ".asv/results",
+
+    // The directory (relative to the current directory) that the html tree
+    // should be written to.  If not provided, defaults to "html".
+    "html_dir": ".asv/html",
+
+    // The number of characters to retain in the commit hashes.
+    // "hash_length": 8,
+
+    // `asv` will cache results of the recent builds in each
+    // environment, making them faster to install next time.  This is
+    // the number of builds to keep, per environment.
+    // "build_cache_size": 2,
+
+    // The commits after which the regression search in `asv publish`
+    // should start looking for regressions. Dictionary whose keys are
+    // regexps matching to benchmark names, and values corresponding to
+    // the commit (exclusive) after which to start looking for
+    // regressions.  The default is to start from the first commit
+    // with results. If the commit is `null`, regression detection is
+    // skipped for the matching benchmark.
+    //
+    // "regressions_first_commits": {
+    //    "some_benchmark": "352cdf",  // Consider regressions only after this commit
+    //    "another_benchmark": null,   // Skip regression detection altogether
+    // },
+
+    // The thresholds for relative change in results, after which `asv
+    // publish` starts reporting regressions. Dictionary of the same
+    // form as in ``regressions_first_commits``, with values
+    // indicating the thresholds.  If multiple entries match, the
+    // maximum is taken. If no entry matches, the default is 5%.
+    //
+    // "regressions_thresholds": {
+    //    "some_benchmark": 0.01,     // Threshold of 1%
+    //    "another_benchmark": 0.5,   // Threshold of 50%
+    // },
+}