Merge branch 'release/0.6.0'

.gitattributes

@@ -1 +1,2 @@
-benchmarks/storage/*.json filter=lfs diff=lfs merge=lfs -text
+benchmarks/storage/*.db filter=lfs diff=lfs merge=lfs -text
+*.ipynb linguist-generated

.github/contributing.md

@@ -5,6 +5,24 @@ contributions guidelines](.github/contributing.md#external-contributions)
 
 ## Internal development
 
+### Release based workflow
+
+The development it's following some conventions to improve collaboration:
+
+- the _almost_ standard [SemVer](https://semver.org/) it's adopted for versions'
+  numbers
+- the popular [git flow
+  model](https://nvie.com/posts/a-successful-git-branching-model/) it's used for
+  managing git branches
+  - in order to help you with the management consider using [`git flow`](https://github.com/petervanderdoes/gitflow-avh) CLI tool (and the corresponding [shell completion](https://github.com/petervanderdoes/git-flow-completion)), or the original version of [`git flow`](https://github.com/nvie/gitflow).
+
+#### Caveat
+
+- remember to base all the pull requests on GitHub to `develop` (and not
+  `main`/`master`)
+- while using `git flow` to merge remember to use the `-k` (keep) option, for
+  GitHub compatibility
+
 ### Installation
 
 #### Test Dependencies
@@ -64,17 +82,6 @@ provided scripts, and then select with suitable queries the combinations of
 input you are interested in, and running the benchmark utility passing the
 queries as arguments.
 
-### Release based workflow
-
-Since it is appropriate to develop this code in versions (as in the way
-suggested by [SemVer](https://semver.org/)) we decided to base our workflow on
-the popular [git flow model](https://nvie.com/posts/a-successful-git-branching-model/).
-
-In order to help you with the management consider using [`git flow`](https://github.com/petervanderdoes/gitflow-avh) CLI tool (and the
-corresponding [shell
-completion](https://github.com/petervanderdoes/git-flow-completion)), or the
-original version of [`git flow`](https://github.com/nvie/gitflow).
-
 ## External contributions
 
 Currently the main guideline we would like to highlight is to use [GitHub

.github/workflows/pub_docs.yml

@@ -38,13 +38,21 @@ jobs:
           python -m pip install --upgrade pip
           # install yadism
           pip install .
+          pip install benchmarks/
       - name: Build 🔨
         run: |
           pip install -r doc_requirements.txt
           sudo apt-get install graphviz
+          # the following is required by nbsphinx
+          sudo apt-get install pandoc
+          # install home page dependencies
           cd docs/home-page
           yarn
+          # tags are required for the home page structure
+          git fetch --tags
+          # build the home-page
           make
+          # build sphinx for the current branch
           cd ../sphinx/
           make html
       - name: Save files 💾

.github/workflows/unittests.yml

@@ -49,7 +49,7 @@ jobs:
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v1
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+          #token: ${{ secrets.CODECOV_TOKEN }}
           file: ./coverage.xml
           flags: unittests
           name: codecov-umbrella

.gitignore

@@ -1,6 +1,8 @@
 # ignore version
 src/yadism/version.py
 
+*.wgt
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.pylintrc

@@ -3,7 +3,7 @@
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
 # run arbitrary code
-extension-pkg-whitelist=numpy,lhapdf,QCDNUM,scipy.special,rich
+extension-pkg-whitelist=numpy,lhapdf,apfel,QCDNUM,xspace_bench,scipy.special,pineappl
 
 # Add files or directories to the blacklist. They should be base names, not
 # paths.

.readthedocs.yaml

@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/sphinx/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+# formats:
+# - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.8
+  install:
+    - method: pip
+      path: .
+    - requirements: doc_requirements.txt

README.md

@@ -14,7 +14,7 @@
 /github/workflow/status/N3PDF/dis/yadism
 
 use the ones provided by shields.io:
-- example: https://img.shields.io/github/workflow/status/N3PDF/dis/yadism
+- example: https://img.shields.io/github/workflow/status/N3PDF/yadism
 
 note: in order to make shields.io the repo must be public (or accessible to it in some way)
 
@@ -51,7 +51,7 @@ python setup.py install
 The documentation style of this code follows closely the [numpy documentation
 guide](https://numpydoc.readthedocs.io/en/latest/format.html).
 
-Docs available at: https://n3pdf.github.io/dis/
+Docs available at: https://n3pdf.github.io/yadism/
 
 ## Development
 
@@ -67,3 +67,4 @@ an email to the authors:
 
 - [Alessandro Candido](mailto:[email protected])
 - [Felix Hekhorn](mailto:[email protected])
+- [Giacomo Magni](mailto:[email protected])

benchmarks/.gitignore

@@ -1 +1,5 @@
+# ignore qcdnum weights' files
 *.wgt
+# ignore airspeed velocity output
+html/
+results/

benchmarks/asv.conf.json

@@ -0,0 +1,84 @@
+{
+    // 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": "yadism",
+
+    // The project's homepage
+    "project_url": "https://n3pdf.github.io/yadism/",
+
+    // The URL or local path of the source code repository for the
+    // project being benchmarked
+    "repo": "..",
+
+    // List of branches to benchmark. If not provided, defaults to "master"
+    // (for git) or "tip" (for mercurial).
+    "branches": ["HEAD"],
+
+    // 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" 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",
+
+    // the base URL to show a commit for the project.
+    "show_commit_url": "https://github.com/N3PDF/yadism/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"],
+
+    // The matrix of dependencies to test.  Each key is the name of a
+    // package (in PyPI) and the values are version numbers.  An empty
+    // list indicates to just test against the default (latest)
+    //version.
+    "matrix": {
+        "packutil": []
+    },
+
+    // The directory (relative to the current directory) that benchmarks are
+    // stored in.  If not provided, defaults to "benchmarks"
+    "benchmark_dir": "performance",
+
+    // The directory (relative to the current directory) to cache the Python
+    // environments in.  If not provided, defaults to "env"
+    "env_dir": "../env",
+
+    // The directory (relative to the current directory) that raw benchmark
+    // results are stored in.  If not provided, defaults to "results".
+    "results_dir": "results",
+
+    // The directory (relative to the current directory) that the html tree
+    // should be written to.  If not provided, defaults to "html".
+    "html_dir": "html",
+
+    // The number of characters to retain in the commit hashes.
+    // "hash_length": 8,
+
+    // `asv` will cache wheels of the recent builds in each
+    // environment, making them faster to install next time.  This is
+    // number of builds to keep, per environment.
+    "build_cache_size": 8
+
+    // 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
+    // }
+}

benchmarks/performance/__init__.py

@@ -0,0 +1 @@
+

benchmarks/performance/benchmarks.py

@@ -0,0 +1,35 @@
+# Write the benchmarking functions here.
+# See "Writing benchmarks" in the asv docs for more information.
+
+import numpy as np
+
+
+class TimeSuite:
+    """
+    An example benchmark that times the performance of various kinds
+    of iterating over dictionaries in Python.
+    """
+
+    def setup(self):
+        self.d = {}
+        for x in range(500):
+            self.d[x] = None
+
+    def time_keys(self):
+        for key in self.d.keys():
+            pass
+
+    def time_range(self):
+        d = self.d
+        for key in range(500):
+            x = d[key]
+
+    def time_arange(self):
+        d = self.d
+        for key in np.arange(500):
+            x = d[key]
+
+
+class MemSuite:
+    def mem_list(self):
+        return [0] * 256