BM8 comparison page using Jupyter

.github/workflows/test-pfhub-package.yml

@@ -0,0 +1,21 @@
+name: Test PFHub Package
+on: [push, pull_request]
+jobs:
+  pfhub-nix-test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ./_data/python-pfhub
+    steps:
+      - uses: actions/checkout@v2.3.4
+      - uses: cachix/install-nix-action@v14.1
+        with:
+          nix_path: nixpkgs=channel:nixos-unstable
+          name: pfhub
+          authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+          extraPullNames: nix-community
+      - run: nix-shell --pure --command "py.test --nbval-lax --cov-fail-under=100"
+      - run: nix-shell --pure --command "black --check setup.py pfhub"
+      - run: nix-shell --pure --command "pylint setup.py pfhub"
+      - run: nix-shell --pure --command "flake8 setup.py pfhub"
+      - run: nix-shell --pure --command "py.test --nbval-lax ../../results/benchmark*.ipynb"

.gitignore

@@ -8,3 +8,5 @@ _apps/data/env_variables.yaml
 _apps/box/1014649_e91k0tua_config.json
 _apps/box/cert.pem
 _apps/box/.coverage
+.~*
+_data/pfhub/.coverage

.travis.yml

@@ -40,7 +40,7 @@ script:
       make notebooks &&
       rm -rf ./_site &&
       jekyll build -d ./_site/pfhub && htmlproofer --check-html --only-4xx --allow-hash-href --empty-alt-ignore --checks-to-ignore ImageCheck --file-ignore ./_site/pfhub/node_modules ./_site &&
-      py.test --ignore=hackathons/hackathon1 --ignore=benchmarks --ignore=_data --nbval --sanitize-with sanitize.cfg &&
+      py.test --ignore=hackathons/hackathon1 --ignore=benchmarks --ignore=_data --nbval --sanitize-with sanitize.cfg --ignore=results &&
       coffeelint _includes/coffee/ &&
       mocha _site/pfhub/js/test.js
     ";

Makefile

@@ -17,6 +17,10 @@ $(HEXBIN_OUT): $(HEXBIN_IN)
 
 %.ipynb.raw.html: %.ipynb
 	jupyter-nbconvert $< --output $(notdir $@) --to html --template basic
+	if [ "results/"  = "$(dir $@)" ]; then \
+	  sed -i '1i {\% raw \%}' $@; \
+	  sed -i  -e '$$a{\% endraw \%}' $@; \
+	fi
 
 %.ipynb.md: %.ipynb
 	cp -n ./template.ipynb.md $@

_data/python-pfhub/.coveragerc

@@ -0,0 +1,2 @@
+[run]
+omit = pfhub/__init__.py

_data/python-pfhub/.pylintrc

@@ -0,0 +1,8 @@
+[MASTER]
+extension-pkg-whitelist = numpy
+
+[TYPECHECK]
+ignored-modules = numpy, toolz.curried
+
+[MESSAGES CONTROL]
+disable = no-value-for-parameter, bad-continuation

_data/python-pfhub/README.md

@@ -0,0 +1,29 @@
+# Python-PFHub
+
+A Python module for rendering PFHub phase field data in Jupyter
+notebooks using Pandas and Plotly.
+
+## Installation
+
+### Using Nix
+
+If Using Cachix
+
+    $ cachix use pfhub
+
+and then fire up a Nix shell with
+
+    $ export NIX_VERSION=21.05
+    $ nix-shell \
+        -I nixpkgs=https://github.com/NixOS/nixpkgs/archive/${NIX_VERSION}.tar.gz \
+        -I pfhub=./ \
+        -E 'with (import <nixpkgs> {}); mkShell { buildInputs = [ (python3Packages.callPackage <pfhub> { }) ]; }'
+
+#### Upload to cachix
+
+    $ export NIX_VERSION=21.05
+    $ nix-build \
+        -I nixpkgs=https://github.com/NixOS/nixpkgs/archive/${NIX_VERSION}.tar.gz \
+        -I pfhub=./ \
+        -E 'with (import <nixpkgs> {}); python3Packages.callPackage <pfhub> { }' \
+        | cachix push pfhub

_data/python-pfhub/default.nix

@@ -0,0 +1,49 @@
+{ lib
+, buildPythonPackage
+, pytestCheckHook
+, python
+, numpy
+, pytest
+, toolz
+, pyyaml
+, pandas
+, plotly
+, pytestcov
+, jupyter
+, nbval
+}:
+buildPythonPackage rec {
+  pname = "pfhub";
+  version = "0.1";
+
+  src = lib.cleanSource ./.;
+
+  propagatedBuildInputs = [
+    numpy
+    pytest
+    toolz
+    pyyaml
+    pandas
+    plotly
+    pytestcov
+    jupyter
+    nbval
+  ];
+
+  checkInputs = [
+    python
+  ];
+
+  checkPhase = ''
+    ${python.interpreter} -c "import pfhub; pfhub.test()"
+  '';
+
+  pythonImportsCheck = ["pfhub"];
+
+  meta = with lib; {
+    homepage = "https://github.com/usnistgov/pfhub";
+    description = "The Phase Field Community Hub";
+    license = licenses.mit;
+    maintainers = with maintainers; [ wd15 ];
+  };
+}

_data/python-pfhub/notebooks/sanitize.cfg

@@ -0,0 +1,11 @@
+[regex]
+regex: '#[-0-9a-z]{36}'
+replace: '#'
+
+[regex]
+regex: "[-0-9a-z]{36}"
+replace: ""
+
+[regex]
+regex: '[-0-9a-z]{36}'
+replace: ''

_data/python-pfhub/pfhub/__init__.py

@@ -0,0 +1,28 @@
+"""PFHub - Phase Field Community Hub
+
+See the documentation at https://github.com/usnistgov/pfhub
+"""
+
+
+import os
+
+
+def test(*args):
+    r"""Run all the module tests.
+
+    Equivalent to running ``py.test pfhub`` in the base
+
+    Args:
+      *args: add arguments to pytest
+
+    To test an installed version of PFHub use
+
+    .. code-block:: bash
+
+       $ python -c "import pfhub; pfhub.test()"
+
+    """
+    import pytest  # pylint: disable=import-outside-toplevel
+
+    path = os.path.join(os.path.split(__file__)[0])
+    pytest.main(args=[path, "--doctest-modules", "-r s"] + list(args))

_data/python-pfhub/pfhub/conftest.py

@@ -0,0 +1,112 @@
+"""Setup for pytest
+"""
+
+import pytest
+
+
+def make_yaml_content(id_, version):
+    """Generate some test yaml content
+
+    Args:
+      id_: the benchmark id_ (e.g. "8a")
+      version: the version (e.g. "1")
+
+    Returns:
+      yaml result content as string
+    """
+    return f"""
+---
+benchmark:
+  id: {id_}
+  version: {version}
+metadata:
+  implementation:
+    name: code_name
+  author:
+    first: first
+    last: last
+  timestamp: 2021-12-07
+data:
+  - name: free_energy
+    type: line
+    values:
+      - x: 0.0
+        y: 0.0
+        z: 0.0
+      - x: 1.0
+        y: 1.0
+        z: 1.0
+    transform:
+      - type: formula
+        expr: datum.x
+        as: a
+      - type: formula
+        expr: datum.y * 2
+        as: b
+"""
+
+
+def make_yaml(dir_, name, id_, version):
+    """Generate a yaml file for test purposes
+
+    Args:
+      dir_: the result directory to write to
+      name: name of the result
+      id_: the benchmark id_ (e.g. "8a")
+      version: the version (e.g. "1")
+
+    Returns:
+      name of the file created
+    """
+    dir_name = dir_ / name
+    dir_name.mkdir(exist_ok=True)
+    yaml_file = dir_name / "meta.yaml"
+    yaml_file.write_text(make_yaml_content(id_, version))
+    return yaml_file
+
+
+@pytest.fixture
+def yaml_data_file(tmp_path):
+    """Generate a yaml test file
+
+    Args:
+      tmp_path: temporary area to use to write files
+
+    Returns:
+      name of the data file
+    """
+    tmp_path.mkdir(exist_ok=True)
+    return make_yaml(tmp_path, "result", "1a", 1)
+
+
+@pytest.fixture
+def test_data_path(tmp_path):
+    """Generate two result data files
+
+    Args:
+      tmp_path: temporary area to use to write files
+
+    Returns:
+      the name of the directory used for writing the files
+    """
+    dir_ = tmp_path / "results"
+    dir_.mkdir(exist_ok=True)
+    make_yaml(dir_, "result1", "1a", 1)
+    make_yaml(dir_, "result2", "2a", 1)
+    return dir_
+
+
+@pytest.fixture
+def csv_file(tmp_path):
+    """Generate a csv file for test purposes
+
+    Args:
+      tmp_path: temporary area to use to write files
+
+    Returns:
+      path to the csv file
+    """
+    tmp_path.mkdir(exist_ok=True)
+    csv_file_path = tmp_path / "file.csv"
+    csv_file_path.write_text("x,y\n0,0\n1,1\n")
+    return csv_file_path