Merge branch 'master' into feat/assertExpectedDataAPI

.github/workflows/ci.yml

@@ -21,13 +21,11 @@ jobs:
       || (github.event_name == 'push' && github.ref != 'refs/heads/master' && contains(github.event.head_commit.message, '[ci all]'))
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: [3.7, 3.8, 3.9]
-        exclude:
+        os: [ubuntu-latest]
+        python-version: ['3.7', '3.8', '3.9']
+        include:
           - os: macos-latest
-            python-version: 3.7
-          - os: macos-latest
-            python-version: 3.8
+            python-version: '3.9'
 
     steps:
     - uses: actions/checkout@v2
@@ -50,7 +48,7 @@ jobs:
         pytest -r sx --ignore tests/benchmarks/ --ignore tests/contrib --ignore tests/test_notebooks.py
 
     - name: Report core project coverage with Codecov
-      if: github.event_name != 'schedule' && matrix.python-version == 3.9 && matrix.os == 'ubuntu-latest'
+      if: github.event_name != 'schedule' && matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'
       uses: codecov/codecov-action@v2
       with:
         files: ./coverage.xml
@@ -61,24 +59,24 @@ jobs:
         pytest -r sx tests/contrib --mpl --mpl-baseline-path tests/contrib/baseline
 
     - name: Report contrib coverage with Codecov
-      if: github.event_name != 'schedule' && matrix.python-version == 3.9 && matrix.os == 'ubuntu-latest'
+      if: github.event_name != 'schedule' && matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'
       uses: codecov/codecov-action@v2
       with:
         files: ./coverage.xml
         flags: contrib
 
     - name: Test docstring examples with doctest
-      if: matrix.python-version == 3.9
+      if: matrix.python-version == '3.9'
       run: pytest -r sx src/ README.rst
 
     - name: Report doctest coverage with Codecov
-      if: github.event_name != 'schedule' && matrix.python-version == 3.9 && matrix.os == 'ubuntu-latest'
+      if: github.event_name != 'schedule' && matrix.python-version == '3.9' && matrix.os == 'ubuntu-latest'
       uses: codecov/codecov-action@v2
       with:
         files: ./coverage.xml
         flags: doctest
 
     - name: Run benchmarks
-      if: github.event_name == 'schedule' && matrix.python-version == 3.9
+      if: github.event_name == 'schedule' && matrix.python-version == '3.9'
       run: |
         pytest -r sx --benchmark-sort=mean tests/benchmarks/test_benchmark.py

.github/workflows/dependencies-head.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.9]
+        python-version: ['3.9']
 
     steps:
     - uses: actions/checkout@v2
@@ -39,7 +39,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.9]
+        python-version: ['3.9']
 
     steps:
     - uses: actions/checkout@v2
@@ -69,7 +69,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.9]
+        python-version: ['3.9']
 
     steps:
     - uses: actions/checkout@v2
@@ -95,7 +95,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.9]
+        python-version: ['3.9']
 
     steps:
     - uses: actions/checkout@v2
@@ -120,7 +120,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.9]
+        python-version: ['3.9']
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/docs.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ['3.9']
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/lint.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.9'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools wheel

.github/workflows/lower-bound-requirements.yml

@@ -14,7 +14,7 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         # minimum supported Python
-        python-version: [3.7]
+        python-version: ['3.7']
 
     steps:
     - uses: actions/checkout@v2
@@ -27,9 +27,7 @@ jobs:
     - name: Install dependencies and force lowest bound
       run: |
         python -m pip install --upgrade pip setuptools wheel
-        python -m pip --no-cache-dir --quiet install --requirement lower-bound-requirements.txt
-        python -m pip --no-cache-dir --quiet install .[test]
-        python -m pip install --requirement lower-bound-requirements.txt
+        python -m pip --no-cache-dir install --constraint tests/constraints.txt .[test]
 
     - name: List installed Python packages
       run: python -m pip list

.github/workflows/notebooks.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.9]
+        python-version: ['3.9']
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/publish-package.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.9'
 
     - name: Install python-build, check-manifest, and twine
       run: |

.github/workflows/release_tests.yml

@@ -14,10 +14,10 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ['3.7', '3.8', '3.9']
         include:
           - os: macos-latest
-            python-version: 3.9
+            python-version: '3.9'
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/tag.yml

@@ -61,7 +61,7 @@ jobs:
     - name: Set up Python 3.9
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
+        python-version: '3.9'
     - name: Install bump2version
       run: |
         python -m pip install --upgrade pip setuptools wheel

.pre-commit-config.yaml

@@ -20,13 +20,12 @@ repos:
       exclude: ^validation/|\.dtd$|\.json$|\.xml$
     - id: mixed-line-ending
     - id: requirements-txt-fixer
-      exclude: lower-bound-requirements.txt
     - id: trailing-whitespace
       # exclude generated files
       exclude: ^validation/|\.dtd$|\.xml$
 
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v2.29.0
+    rev: v2.29.1
     hooks:
     - id: pyupgrade
       args: ["--py37-plus"]
@@ -37,26 +36,26 @@ repos:
     - id: absolufy-imports
 
 -   repo: https://github.com/psf/black
-    rev: 21.10b0
+    rev: 21.12b0
     hooks:
     - id: black-jupyter
 
 -   repo: https://github.com/asottile/blacken-docs
-    rev: v1.11.0
+    rev: v1.12.0
     hooks:
     - id: blacken-docs
-      additional_dependencies: [black==21.10b0]
+      additional_dependencies: [black==21.12b0]
 
 -   repo: https://github.com/PyCQA/flake8
     rev: 4.0.1
     hooks:
     - id: flake8
 
 -   repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.1.1
+    rev: 1.2.2
     hooks:
     - id: nbqa-pyupgrade
-      additional_dependencies: [pyupgrade==2.29.0]
+      additional_dependencies: [pyupgrade==2.29.1]
 
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.1.0

docs/examples/notebooks/ImpactPlot.ipynb

@@ -25,6 +25,13 @@
     "## Download the Model\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "For this example we'll download the archive of probability models for the ATLAS analysis [JHEP 12 (2019) 060, 2019](https://inspirehep.net/literature/1748602) from its [HEPData page](https://www.hepdata.net/record/ins1748602) using its [specific DOI](https://www.hepdata.net/record/resource/1935437?landing_page=true). You can download this multiple ways, but for simplicity we'll download it using the `pyhf contrib download` command."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
@@ -34,14 +41,25 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "RegionA/BkgOnly.json\n",
-      "RegionA/patch.sbottom_750_745_60.json\n"
+      "\u001b[01;34m1Lbb-probability-models\u001b[00m\n",
+      "├── README.md\n",
+      "├── \u001b[01;34mRegionA\u001b[00m\n",
+      "│   ├── BkgOnly.json\n",
+      "│   └── patchset.json\n",
+      "├── \u001b[01;34mRegionB\u001b[00m\n",
+      "│   ├── BkgOnly.json\n",
+      "│   └── patchset.json\n",
+      "└── \u001b[01;34mRegionC\u001b[00m\n",
+      "    ├── BkgOnly.json\n",
+      "    └── patchset.json\n",
+      "\n",
+      "3 directories, 7 files\n"
      ]
     }
    ],
    "source": [
-    "!curl -sL https://doi.org/10.17182/hepdata.89408.v1/r2  | tar -O -xzv RegionA/BkgOnly.json > lhood.json\n",
-    "!curl -sL https://doi.org/10.17182/hepdata.89408.v1/r2  | tar -O -xzv RegionA/patch.sbottom_750_745_60.json > patch.json"
+    "! pyhf contrib download https://doi.org/10.17182/hepdata.89408.v3/r2 1Lbb-probability-models\n",
+    "! tree 1Lbb-probability-models"
    ]
   },
   {
@@ -58,8 +76,11 @@
    "outputs": [],
    "source": [
     "def make_model(channel_list):\n",
-    "    spec = json.load(open(\"lhood.json\"))\n",
-    "    patch = json.load(open(\"patch.json\"))\n",
+    "    spec = json.load(open(\"1Lbb-probability-models/RegionA/BkgOnly.json\"))\n",
+    "    patchset = pyhf.PatchSet(\n",
+    "        json.load(open(\"1Lbb-probability-models/RegionA/patchset.json\"))\n",
+    "    )\n",
+    "    patch = patchset[\"sbottom_750_745_60\"]\n",
     "    spec = jsonpatch.apply_patch(spec, patch)\n",
     "    spec[\"channels\"] = [c for c in spec[\"channels\"] if c[\"name\"] in channel_list]\n",
     "\n",

pyproject.toml

@@ -38,6 +38,8 @@ ignore = [
     'AUTHORS',
 ]
 
+[tool.pytest]
+xfail_strict = true
 
 [tool.pytest.ini_options]
 minversion = "6.0"

setup.py

@@ -3,13 +3,13 @@
 extras_require = {
     'shellcomplete': ['click_completion'],
     'tensorflow': [
-        'tensorflow~=2.3,!=2.3.0',  # c.f. https://github.com/tensorflow/tensorflow/pull/40789
-        'tensorflow-probability~=0.11',
+        'tensorflow>=2.3.1',  # c.f. https://github.com/tensorflow/tensorflow/pull/40789
+        'tensorflow-probability>=0.11.0',  # c.f. PR #1657
     ],
-    'torch': ['torch~=1.10'],
+    'torch': ['torch>=1.10.0'],  # c.f. PR #1657
     'jax': ['jax>=0.2.10', 'jaxlib>=0.1.60,!=0.1.68'],  # c.f. Issue 1501
-    'xmlio': ['uproot>=4.1.1'],
-    'minuit': ['iminuit>=2.4'],
+    'xmlio': ['uproot>=4.1.1'],  # c.f. PR #1567
+    'minuit': ['iminuit>=2.4.0'],  # c.f. PR #1306
 }
 extras_require['backends'] = sorted(
     set(
@@ -29,9 +29,11 @@
         + extras_require['contrib']
         + extras_require['shellcomplete']
         + [
-            'pytest~=6.0',
+            'scikit-hep-testdata>=0.4.11',
+            'pytest>=6.0',
             'pytest-cov>=2.5.1',
             'pytest-mock',
+            'requests-mock>=1.9.0',
             'pytest-benchmark[histogram]',
             'pytest-console-scripts',
             'pytest-mpl',

src/pyhf/cli/complete.py

@@ -16,7 +16,6 @@ def cli(shell):
         '''Generate shell completion code for various shells.'''
         click.echo(click_completion.core.get_code(shell, prog_name='pyhf'))
 
-
 except ImportError:
 
     @click.command(help='Generate shell completion code.', name='completions')