Faster CI: Remove C++ from the CI and reduce the number of installed …

…packages. (#99)

* Minimal CI.

* Remove Bazel references. Fix cosign github action.

* Add pip to environment-ci.yml

.github/workflows/docker-publish.yml

@@ -64,9 +64,9 @@ jobs:
       # https://github.com/sigstore/cosign-installer
       - name: Install cosign
         if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@7e0881f8fe90b25e305bbf0309761e9314607e25
+        uses: sigstore/cosign-installer@f3c664df7af409cb4873aa5068053ba9d61a57b6 #v2.6.0
         with:
-          cosign-release: "v1.9.0"
+          cosign-release: "v1.11.0"
 
       # Workaround: https://github.com/docker/build-push-action/issues/461
       - name: Setup Docker buildx

.github/workflows/test.yml

@@ -31,7 +31,6 @@ jobs:
     # https://github.com/marketplace/actions/setup-miniconda#caching-environments
     steps:
       - uses: actions/checkout@v2
-      - uses: bazelbuild/setup-bazelisk@v2
       - name: Setup Mambaforge
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -47,42 +46,23 @@ jobs:
       - name: Cache Dependencies
         uses: actions/cache@v2
         with:
-          # Cache the Conda, Bazel, and Pre-commit files
+          # Cache the Conda, and Pre-commit files
           path: |
             ${{ env.CONDA }}/envs
             ~/.cache/pre-commit
-            ~/.cache/bazel
-          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('environment.yml') }}-${{ env.CACHE_NUMBER }}
+          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('environment-ci.yml') }}-${{ env.CACHE_NUMBER }}
         env:
-          # Increase this value to reset cache if environment.yml has not changed
+          # Increase this value to reset cache if environment-ci.yml has not changed
           CACHE_NUMBER: 1
         id: cache
       - name: Update environment
-        run: mamba env update -n anaconda-client-env -f environment.yml
+        run: mamba env update -n anaconda-client-env -f environment-ci.yml
         if: steps.cache.outputs.cache-hit != 'true'
       - name: Run all pre-commit checks on the full repo!
         run: |
           pre-commit run --all-files
-      - name: Build and install pyimprint
-        run: |
-          cd imprint
-          ./generate_bazelrc
-          # this is to see if installation via wheel works
-          bazel build -c dbg //python:pyimprint_wheel
-          pip install --no-deps --force-reinstall bazel-bin/python/dist/*.whl
-          # this is to see if editable installation works
-          # the pip install -e is not run until ./install.sh in the next step.
-          bazel build -c dbg //python:pyimprint/core.so
-          # Unfortunately, using a symlink doesn't work here for reasons that I
-          # don't understand
-          # ln -sf ./bazel-bin/python/pyimprint/core.so python/pyimprint/core.so
-          cp ./bazel-bin/python/pyimprint/core.so python/pyimprint/core.so
       - name: Install our libraries
         run: ./install.sh
-      - name: Bazel Test
-        run: |
-          cd imprint
-          bazel test -c dbg //...
       - name: Pytest
         run: |
           pytest .

.vscode/settings.json

@@ -1,5 +1,4 @@
 {
-  "bazel-cpp-tools.compileCommands.targets": ["//..."],
   "jupyter.jupyterServerType": "local",
   "files.associations": {
     "functional": "cpp",

confirm/confirm/mini_imprint/grid.py

@@ -12,7 +12,7 @@
 class HyperPlane:
     """
     A plane defined by:
-    x \cdot n - c = 0
+    x.dot(n) - c = 0
 
     Sign convention: When used as the boundary between null hypothesis and
     alternative, the normal should point towards the null hypothesis space.

confirm/tests/test_berry.py

@@ -173,7 +173,7 @@ def test_inla_properties(method):
     np.testing.assert_allclose(sigma2_integral, 1.0)
 
 
-@pytest.mark.parametrize("method", ["jax", "numpy", "cpp"])
+@pytest.mark.parametrize("method", ["jax", "numpy"])
 def test_fast_inla(method, N=10, iterations=1):
     n_i = np.tile(np.array([20, 20, 35, 35]), (N, 1))
     y_i = np.tile(np.array([0, 1, 9, 10], dtype=np.float64), (N, 1))
@@ -251,87 +251,6 @@ def test_fast_inla_same_results(N=1, iterations=1_000):
             )
 
 
-def test_py_binomial(n_arms=2, n_theta_1d=16, sim_size=100):
-    """
-    Test against the Imprint accumulation and bound routines.
-    """
-    import pyimprint.grid as grid
-    from pyimprint.bound import TypeIErrorBound
-    from pyimprint.driver import accumulate_process
-    from pyimprint.model.binomial import SimpleSelection
-    from confirm.berrylib.imprint import BerryImprintModel
-
-    n_arm_samples = 35
-    seed = 10
-    # getting an exact match is only possible with n_threads = 1 because
-    # parallelism in the imprint accumulator leads to a different order of random
-    # numbers.
-    n_threads = 1
-
-    # define null hypos
-    null_hypos = []
-    for i in range(n_arms):
-        n = np.zeros(n_arms)
-        # null is:
-        # theta_i <= logit(0.1)
-        # the normal should point towards the negative direction. but that also
-        # means we need to negate the logit(0.1) offset
-        n[i] = -1
-        null_hypos.append(grid.HyperPlane(n, -logit(0.1)))
-    gr = grid.make_cartesian_grid_range(
-        n_theta_1d, np.full(n_arms, -3.5), np.full(n_arms, 1.0), sim_size
-    )
-    gr.create_tiles(null_hypos)
-    gr.prune()
-    n_tiles = gr.n_tiles()
-
-    fi = fast_inla.FastINLA(n_arms=n_arms)
-    b = BerryImprintModel(fi, n_arm_samples, [0.85])
-    acc_o = accumulate_process(b, gr, sim_size, seed, n_threads)
-
-    np.random.seed(seed)
-    samples = np.random.uniform(size=(sim_size, n_arm_samples, n_arms))
-
-    theta_tiles = grid.theta_tiles(gr)
-    nulls = grid.is_null_per_arm(gr)
-
-    accumulator = binomial.binomial_accumulator(fi.rejection_inference)
-    typeI_sum, typeI_score = accumulator(theta_tiles, nulls, samples)
-    assert np.all(typeI_sum.to_py() == acc_o.typeI_sum()[0])
-    np.testing.assert_allclose(
-        typeI_score.to_py(), acc_o.score_sum().reshape(n_tiles, n_arms), 1e-4
-    )
-
-    corners = grid.collect_corners(gr)
-    tile_radii = grid.radii_tiles(gr)
-    sim_sizes = grid.sim_sizes_tiles(gr)
-    total, d0, d0u, d1w, d1uw, d2uw = binomial.upper_bound(
-        theta_tiles,
-        tile_radii,
-        corners,
-        sim_sizes,
-        n_arm_samples,
-        typeI_sum.to_py(),
-        typeI_score.to_py(),
-    )
-
-    delta = 0.025
-    critvals = np.array([0.99])
-    simple_selection_model = SimpleSelection(fi.n_arms, n_arm_samples, 1, critvals)
-    simple_selection_model.critical_values([fi.critical_value])
-
-    ub = TypeIErrorBound()
-    kbs = simple_selection_model.make_imprint_bound_state(gr)
-    ub.create(kbs, acc_o, gr, delta)
-
-    np.testing.assert_allclose(d0, ub.delta_0()[0])
-    np.testing.assert_allclose(d0u, ub.delta_0_u()[0])
-    np.testing.assert_allclose(d1w, ub.delta_1()[0], rtol=1e-05)
-    np.testing.assert_allclose(d1uw, ub.delta_1_u()[0])
-    np.testing.assert_allclose(d2uw, ub.delta_2_u()[0])
-    np.testing.assert_allclose(total, ub.get()[0])
-
-
 def test_rejection_table():
     fi = fast_inla.FastINLA(n_arms=2)
     n = 10

install.sh

@@ -9,15 +9,8 @@ fi
 # Set up pre-commit so it's fast the first time it gets used
 pre-commit install --install-hooks
 
-pushd imprint || exit
-./generate_bazelrc
-popd || exit
-
 # List the internal packages that should be available here.
-for PKG in ./confirm ./imprint/python
-do
-    [ -d "$PKG" ] && echo -e "\nDirectory $PKG exists. Installing... \n" && pip install --no-deps -e "$PKG"
-done
+pip install --no-deps -e ./confirm
 
 # Set up our imprint remote so we can use subtree. On Codespaces, we need
 # https. Locally, we use ssh.