From 117c56482909cea28418773f486c6c4bc6bf6574 Mon Sep 17 00:00:00 2001
From: Marco Gorelli <m.e.gorelli@gmail.com>
Date: Thu, 26 Nov 2020 10:17:51 +0000
Subject: [PATCH 1/7] put test_distributions in separate job

---
 .github/workflows/pytest.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 66474705a96..5b226d0c799 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -30,6 +30,7 @@ jobs:
             --ignore=pymc3/tests/test_gp.py
             --ignore=pymc3/tests/test_shape_handling
             --ignore=pymc3/tests/test_quadpotential.py
+            --ignore=pymc3/tests/test_distributions.py
           - |
             pymc3/tests/test_distributions_random.py
             pymc3/tests/test_shared.py
@@ -49,6 +50,8 @@ jobs:
             pymc3/tests/test_variational_inference.py
             pymc3/tests/test_updates.py
             pymc3/tests/test_shape_handling.py
+          - |
+            pymc3/tests/test_distributions.py
     runs-on: ${{ matrix.os }}
     env:
       TEST_SUBSET: ${{ matrix.test-subset }}

From a72e1f9f15d28ad0745f50cc01a8915ff1c9e2fa Mon Sep 17 00:00:00 2001
From: Marco Gorelli <m.e.gorelli@gmail.com>
Date: Thu, 26 Nov 2020 10:27:29 +0000
Subject: [PATCH 2/7] :art: sort

---
 .github/workflows/pytest.yml | 40 ++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 5b226d0c799..551bf98b2ec 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -14,42 +14,42 @@ jobs:
         floatx: [float32, float64]
         test-subset:
           - |
-            --ignore=pymc3/tests/test_examples.py
-            --ignore=pymc3/tests/test_distributions_random.py
-            --ignore=pymc3/tests/test_variational_inference.py
-            --ignore=pymc3/tests/test_shared.py
-            --ignore=pymc3/tests/test_smc.py
-            --ignore=pymc3/tests/test_updates.py
-            --ignore=pymc3/tests/test_posteriors.py
-            --ignore=pymc3/tests/test_sampling.py
-            --ignore=pymc3/tests/test_parallel_sampling.py
             --ignore=pymc3/tests/test_dist_math.py
             --ignore=pymc3/tests/test_distribution_defaults.py
+            --ignore=pymc3/tests/test_distributions.py
+            --ignore=pymc3/tests/test_distributions_random.py
             --ignore=pymc3/tests/test_distributions_timeseries.py
-            --ignore=pymc3/tests/test_random.py
+            --ignore=pymc3/tests/test_examples.py
             --ignore=pymc3/tests/test_gp.py
-            --ignore=pymc3/tests/test_shape_handling
+            --ignore=pymc3/tests/test_parallel_sampling.py
+            --ignore=pymc3/tests/test_posteriors.py
             --ignore=pymc3/tests/test_quadpotential.py
-            --ignore=pymc3/tests/test_distributions.py
+            --ignore=pymc3/tests/test_random.py
+            --ignore=pymc3/tests/test_sampling.py
+            --ignore=pymc3/tests/test_shape_handling
+            --ignore=pymc3/tests/test_shared.py
+            --ignore=pymc3/tests/test_smc.py
+            --ignore=pymc3/tests/test_updates.py
+            --ignore=pymc3/tests/test_variational_inference.py
           - |
-            pymc3/tests/test_distributions_random.py
-            pymc3/tests/test_shared.py
-            pymc3/tests/test_smc.py
-            pymc3/tests/test_sampling.py
-            pymc3/tests/test_parallel_sampling.py
             pymc3/tests/test_dist_math.py
             pymc3/tests/test_distribution_defaults.py
+            pymc3/tests/test_distributions_random.py
             pymc3/tests/test_distributions_timeseries.py
+            pymc3/tests/test_parallel_sampling.py
             pymc3/tests/test_random.py
+            pymc3/tests/test_sampling.py
+            pymc3/tests/test_shared.py
+            pymc3/tests/test_smc.py
           - |
             pymc3/tests/test_examples.py
-            pymc3/tests/test_posteriors.py
             pymc3/tests/test_gp.py
+            pymc3/tests/test_posteriors.py
             pymc3/tests/test_quadpotential.py
           - |
-            pymc3/tests/test_variational_inference.py
-            pymc3/tests/test_updates.py
             pymc3/tests/test_shape_handling.py
+            pymc3/tests/test_updates.py
+            pymc3/tests/test_variational_inference.py
           - |
             pymc3/tests/test_distributions.py
     runs-on: ${{ matrix.os }}

From d37b7b7e64a87f31c6928364405cf7d00b653d63 Mon Sep 17 00:00:00 2001
From: Marco Gorelli <m.e.gorelli@gmail.com>
Date: Thu, 26 Nov 2020 10:27:51 +0000
Subject: [PATCH 3/7] add arviz compat job

---
 .github/workflows/arviz_compat.yml | 45 ++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)
 create mode 100644 .github/workflows/arviz_compat.yml

diff --git a/.github/workflows/arviz_compat.yml b/.github/workflows/arviz_compat.yml
new file mode 100644
index 00000000000..497b7d39df5
--- /dev/null
+++ b/.github/workflows/arviz_compat.yml
@@ -0,0 +1,45 @@
+name: arviz-compatibility
+
+on:
+  pull_request:
+  push:
+    branches: [master]
+
+jobs:
+  pytest:
+    strategy:
+      matrix:
+        python-version: ["3.8"]
+        os: [ubuntu-18.04]
+        floatx: [float64]
+        test-subset:
+          - pymc3/tests/test_sampling.py
+    runs-on: ${{ matrix.os }}
+    env:
+      TEST_SUBSET: ${{ matrix.test-subset }}
+      THEANO_FLAGS: floatX=${{ matrix.floatx }},gcc.cxxflags='-march=native'
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Cache conda
+        uses: actions/cache@v1
+        env:
+          # Increase this value to reset cache if environment-dev.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('environment-dev.yml') }}
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: testenv
+          channel-priority: strict
+          environment-file: environment-dev.yml
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - run: |
+          conda activate testenv
+          conda remove arviz -y
+          pip install git+git://github.com/arviz-devs/arviz.git
+          python -m pytest -v --cov=pymc3 --cov-report=xml --cov-report term --durations=50 $TEST_SUBSET -n auto

From 843dc554bc5b577dcd98cef43ce2747071987f76 Mon Sep 17 00:00:00 2001
From: Marco Gorelli <m.e.gorelli@gmail.com>
Date: Thu, 26 Nov 2020 14:19:18 +0000
Subject: [PATCH 4/7] fix ignored test

---
 .github/workflows/pytest.yml           |  4 +++-
 .pre-commit-config.yaml                | 13 +++++++++----
 scripts/check_all_tests_are_covered.py | 12 ++++++++++++
 3 files changed, 24 insertions(+), 5 deletions(-)
 create mode 100644 scripts/check_all_tests_are_covered.py

diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 551bf98b2ec..89b3ef09df4 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -21,12 +21,13 @@ jobs:
             --ignore=pymc3/tests/test_distributions_timeseries.py
             --ignore=pymc3/tests/test_examples.py
             --ignore=pymc3/tests/test_gp.py
+            --ignore=pymc3/tests/test_mixture.py
             --ignore=pymc3/tests/test_parallel_sampling.py
             --ignore=pymc3/tests/test_posteriors.py
             --ignore=pymc3/tests/test_quadpotential.py
             --ignore=pymc3/tests/test_random.py
             --ignore=pymc3/tests/test_sampling.py
-            --ignore=pymc3/tests/test_shape_handling
+            --ignore=pymc3/tests/test_shape_handling.py
             --ignore=pymc3/tests/test_shared.py
             --ignore=pymc3/tests/test_smc.py
             --ignore=pymc3/tests/test_updates.py
@@ -44,6 +45,7 @@ jobs:
           - |
             pymc3/tests/test_examples.py
             pymc3/tests/test_gp.py
+            pymc3/tests/test_mixture.py
             pymc3/tests/test_posteriors.py
             pymc3/tests/test_quadpotential.py
           - |
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c6ab6619493..278cac0ee76 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -31,14 +31,19 @@ repos:
 - repo: local
   hooks:
     - id: watermark
-      name: Check notebooks have watermark (see Jupyter style guide from PyMC3 Wiki)
-      types: [jupyter]
+      args: [--negate, --multiline]
       entry: '%load_ext watermark.*%watermark -n -u -v -iv -w'
       language: pygrep
-      args: [--negate, --multiline]
       minimum_pre_commit_version: 2.8.0
+      name: Check notebooks have watermark (see Jupyter style guide from PyMC3 Wiki)
+      types: [jupyter]
     - id: check-toc
+      entry: python scripts/check_toc_is_complete.py
+      language: python
       name: Check all notebooks appear in table of contents
       types: [jupyter]
-      entry: python scripts/check_toc_is_complete.py
+    - id: check-no-tests-are-ignored
+      entry: python scripts/check_all_tests_are_covered.py
+      files: ^\.github/workflows/pytest\.yml$
       language: python
+      name: Check no tests are ignored
diff --git a/scripts/check_all_tests_are_covered.py b/scripts/check_all_tests_are_covered.py
new file mode 100644
index 00000000000..7895c20f111
--- /dev/null
+++ b/scripts/check_all_tests_are_covered.py
@@ -0,0 +1,12 @@
+from pathlib import Path
+
+import re
+
+if __name__ == "__main__":
+    pytest_ci_job = Path(".github") / "workflows/pytest.yml"
+    txt = pytest_ci_job.read_text()
+    ignored_tests = set(re.findall(r"(?<=--ignore=)(pymc3/tests.*\.py)", txt))
+    non_ignored_tests = set(re.findall(r"(?<!--ignore=)(pymc3/tests.*\.py)", txt))
+    assert (
+        ignored_tests <= non_ignored_tests
+    ), f"The following tests are ignored by the first job but not run by the others: {ignored_tests.difference(non_ignored_tests)}"

From ecf14b96a3d15560cabb9ad092902426d376a5ef Mon Sep 17 00:00:00 2001
From: Marco Gorelli <m.e.gorelli@gmail.com>
Date: Thu, 26 Nov 2020 14:26:31 +0000
Subject: [PATCH 5/7] document

---
 .pre-commit-config.yaml                | 2 ++
 scripts/check_all_tests_are_covered.py | 9 +++++++++
 2 files changed, 11 insertions(+)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 278cac0ee76..7e3b09244a3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -41,9 +41,11 @@ repos:
       entry: python scripts/check_toc_is_complete.py
       language: python
       name: Check all notebooks appear in table of contents
+      pass_filenames: false
       types: [jupyter]
     - id: check-no-tests-are-ignored
       entry: python scripts/check_all_tests_are_covered.py
       files: ^\.github/workflows/pytest\.yml$
       language: python
       name: Check no tests are ignored
+      pass_filenames: false
diff --git a/scripts/check_all_tests_are_covered.py b/scripts/check_all_tests_are_covered.py
index 7895c20f111..9b4553b3ce9 100644
--- a/scripts/check_all_tests_are_covered.py
+++ b/scripts/check_all_tests_are_covered.py
@@ -1,3 +1,12 @@
+"""
+In .github/workflows/pytest.yml, tests are split between multiple jobs.
+
+Here, we check that the jobs ignored by the first job actually end up getting
+run by the other jobs.
+This is intended to be used as a pre-commit hook, see `.pre-commit-config.yaml`.
+You can run it manually with `pre-commit run check-no-tests-are-ignored --all`.
+"""
+
 from pathlib import Path
 
 import re

From 36e566c331950f872ac21301051a938967b836e2 Mon Sep 17 00:00:00 2001
From: Marco Gorelli <m.e.gorelli@gmail.com>
Date: Thu, 26 Nov 2020 14:30:35 +0000
Subject: [PATCH 6/7] document

---
 scripts/check_all_tests_are_covered.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/scripts/check_all_tests_are_covered.py b/scripts/check_all_tests_are_covered.py
index 9b4553b3ce9..54221fa21bb 100644
--- a/scripts/check_all_tests_are_covered.py
+++ b/scripts/check_all_tests_are_covered.py
@@ -19,3 +19,6 @@
     assert (
         ignored_tests <= non_ignored_tests
     ), f"The following tests are ignored by the first job but not run by the others: {ignored_tests.difference(non_ignored_tests)}"
+    assert (
+        ignored_tests >= non_ignored_tests
+    ), f"The following tests are run by multiple jobs: {non_ignored_tests.difference(ignored_tests)}"

From fdbbc1d67808635ca7c0095c2a2818e23cbe5325 Mon Sep 17 00:00:00 2001
From: Marco Gorelli <m.e.gorelli@gmail.com>
Date: Thu, 26 Nov 2020 15:08:54 +0000
Subject: [PATCH 7/7] noop