From 583c54844f1ed9e438bc32a62901d716b14ee02a Mon Sep 17 00:00:00 2001 From: Jan Date: Wed, 26 Feb 2025 14:38:13 +0100 Subject: [PATCH 01/17] chore: drop Python 3.9 support, update workflows and docs. --- .github/workflows/cd.yml | 9 +- .github/workflows/ci.yml | 3 +- .github/workflows/lint.yml | 11 +- .github/workflows/publish.yml | 2 +- README.md | 4 +- docs/docs/install.md | 2 +- pyproject.toml | 6 +- uv.lock | 3540 +++++++++++++++++++++++++++++++++ 8 files changed, 3557 insertions(+), 20 deletions(-) create mode 100644 uv.lock diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 18b07f1d2..53ef0845e 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -28,16 +28,15 @@ jobs: - name: Install uv and set the python version uses: astral-sh/setup-uv@v5 with: - python-version: '3.9' + python-version: '3.10' enable-cache: true + cache-dependency-glob: "pyproject.toml" - name: Install dependencies with uv - run: | - uv pip install -e .[dev] + run: uv sync --all-extras --dev - name: Run the fast and the slow CPU tests with coverage - run: | - uv run pytest -v -x -n auto -m "not gpu" --cov=sbi --cov-report=xml tests/ + run: uv run pytest -v -x -n auto -m "not gpu" --cov=sbi --cov-report=xml tests/ - name: Upload coverage to Codecov uses: codecov/codecov-action@v4-beta diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 21c3ffa6f..cacffc98d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,7 +20,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.9', '3.12'] + python-version: ['3.10', '3.13'] steps: - name: Checkout @@ -34,6 +34,7 @@ jobs: with: python-version: ${{ matrix.python-version }} enable-cache: true + cache-dependency-glob: "pyproject.toml" - name: Install dependencies with uv run: | diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 412eff315..50d1d2ced 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -22,7 +22,7 @@ jobs: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: '3.9' + python-version: '3.10' - uses: pre-commit/action@v3.0.1 with: extra_args: --all-files --show-diff-on-failure @@ -40,14 +40,11 @@ jobs: - name: Install uv and set the python version uses: astral-sh/setup-uv@v5 with: - python-version: '3.9' + python-version: '3.10' enable-cache: true - name: Install dependencies with uv - run: | - uv pip install torch --extra-index-url https://download.pytorch.org/whl/cpu - uv pip install -e .[dev] + run: uv sync --all-extras --dev - name: Check types with pyright - run: | - uv run pyright sbi + run: uv run pyright sbi diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 89d36eb6a..1d390387f 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -15,7 +15,7 @@ jobs: - name: Set up Python uses: actions/setup-python@v5 with: - python-version: "3.9" + python-version: "3.10" - name: Install pypa/build run: >- python3 -m diff --git a/README.md b/README.md index d25c78970..f209b33aa 100644 --- a/README.md +++ b/README.md @@ -59,14 +59,14 @@ posterior = inference.build_posterior() ### Installation -`sbi` requires Python 3.9 or higher. While a GPU isn't necessary, it can improve +`sbi` requires Python 3.10 or higher. While a GPU isn't necessary, it can improve performance in some cases. We recommend using a virtual environment with [`conda`](https://docs.conda.io/en/latest/miniconda.html) for an easy setup. If `conda` is installed on the system, an environment for installing `sbi` can be created as follows: ``` -conda create -n sbi_env python=3.9 && conda activate sbi_env +conda create -n sbi_env python=3.10 && conda activate sbi_env ``` ### From PyPI diff --git a/docs/docs/install.md b/docs/docs/install.md index 62c058e6a..362a673d5 100644 --- a/docs/docs/install.md +++ b/docs/docs/install.md @@ -1,6 +1,6 @@ # Installation -`sbi` requires Python 3.9 or higher. A GPU is not required, but can lead to +`sbi` requires Python 3.10 or higher. A GPU is not required, but can lead to speed-up in some cases. We recommend using a [`conda`](https://docs.conda.io/en/latest/miniconda.html) virtual environment ([Miniconda installation diff --git a/pyproject.toml b/pyproject.toml index f523f7697..a35f4fb6c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -24,7 +24,7 @@ classifiers = [ "Programming Language :: Python :: 3", "Development Status :: 3 - Alpha", ] -requires-python = ">=3.9" +requires-python = ">=3.10" dynamic = ["version"] readme = "README.md" keywords = ["Bayesian inference", "simulation-based inference", "PyTorch"] @@ -42,7 +42,7 @@ dependencies = [ "tensorboard", "torch>=1.13.0, <2.6.0", "tqdm", - "pymc>=5.0.0", + "pymc>=5.21.0", "zuko>=1.2.0", ] @@ -140,7 +140,7 @@ xfail_strict = true [tool.pyright] include = ["sbi"] exclude = ["**/__pycache__", "**/__node_modules__", ".git", "docs", "tutorials", "tests"] -python_version = "3.9" +python_version = "3.10" reportUnsupportedDunderAll = false reportGeneralTypeIssues = false reportInvalidTypeForm = false diff --git a/uv.lock 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+version = "1.3.1" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "numpy" }, + { name = "torch" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/dc/5b/6d64586668e36678f37d31f4bf75266b7ce606d6159cfbbc2928d9e9d737/zuko-1.3.1.tar.gz", hash = "sha256:00f246802d3f486183185529ba22e0b2bf691397e03b28150a5cf713fa0da758", size = 38939 } +wheels = [ + { url = "https://files.pythonhosted.org/packages/e4/30/d687713138458be81fec8173bd46f5ff21d05aeab9fc6452b6c593d3bf96/zuko-1.3.1-py3-none-any.whl", hash = "sha256:35865355f273e109cd32df2d41c24271349833c4bedf34a7f3870e2872274421", size = 42637 }, +] From 12c034fe207d64e8e5f861f0400038de9ac8ce1e Mon Sep 17 00:00:00 2001 From: Jan Date: Wed, 26 Feb 2025 14:38:45 +0100 Subject: [PATCH 02/17] lint: checks and linting with py3.10. --- sbi/analysis/plot.py | 18 +++++++++++++----- sbi/diagnostics/sbc.py | 6 +++--- sbi/neural_nets/factory.py | 4 ++++ sbi/samplers/mcmc/slice_numpy.py | 2 +- sbi/samplers/vi/vi_divergence_optimizers.py | 6 +++--- sbi/simulators/simutils.py | 2 +- sbi/utils/conditional_density_utils.py | 4 ++-- sbi/utils/diagnostics_utils.py | 2 +- sbi/utils/sbiutils.py | 4 +++- sbi/utils/simulation_utils.py | 2 +- tests/sbiutils_test.py | 4 +++- tests/torchutils_test.py | 2 +- tutorials/08_crafting_summary_statistics.ipynb | 8 ++++---- ...gnostics_simulation_based_calibration.ipynb | 2 +- ..._and_permutation_invariant_embeddings.ipynb | 4 ++-- 15 files changed, 43 insertions(+), 27 deletions(-) diff --git a/sbi/analysis/plot.py b/sbi/analysis/plot.py index 745c55131..e443e57d0 100644 --- a/sbi/analysis/plot.py +++ b/sbi/analysis/plot.py @@ -787,7 +787,9 @@ def pairplot( diag_kwargs_list = to_list_kwargs(diag_kwargs, len(samples)) diag_func = get_diag_funcs(diag_list) diag_kwargs_filled = [] - for i, (diag_i, diag_kwargs_i) in enumerate(zip(diag_list, diag_kwargs_list)): + for i, (diag_i, diag_kwargs_i) in enumerate( + zip(diag_list, diag_kwargs_list, strict=False) + ): diag_kwarg_filled_i = _get_default_diag_kwargs(diag_i, i) # update the defaults dictionary with user provided values diag_kwarg_filled_i = _update(diag_kwarg_filled_i, diag_kwargs_i) @@ -798,7 +800,9 @@ def pairplot( upper_kwargs_list = to_list_kwargs(upper_kwargs, len(samples)) upper_func = get_offdiag_funcs(upper_list) upper_kwargs_filled = [] - for i, (upper_i, upper_kwargs_i) in enumerate(zip(upper_list, upper_kwargs_list)): + for i, (upper_i, upper_kwargs_i) in enumerate( + zip(upper_list, upper_kwargs_list, strict=False) + ): upper_kwarg_filled_i = _get_default_offdiag_kwargs(upper_i, i) # update the defaults dictionary with user provided values upper_kwarg_filled_i = _update(upper_kwarg_filled_i, upper_kwargs_i) @@ -809,7 +813,9 @@ def pairplot( lower_kwargs_list = to_list_kwargs(lower_kwargs, len(samples)) lower_func = get_offdiag_funcs(lower_list) lower_kwargs_filled = [] - for i, (lower_i, lower_kwargs_i) in enumerate(zip(lower_list, lower_kwargs_list)): + for i, (lower_i, lower_kwargs_i) in enumerate( + zip(lower_list, lower_kwargs_list, strict=False) + ): lower_kwarg_filled_i = _get_default_offdiag_kwargs(lower_i, i) # update the defaults dictionary with user provided values lower_kwarg_filled_i = _update(lower_kwarg_filled_i, lower_kwargs_i) @@ -910,7 +916,9 @@ def marginal_plot( diag_kwargs_list = to_list_kwargs(diag_kwargs, len(samples)) diag_func = get_diag_funcs(diag_list) diag_kwargs_filled = [] - for i, (diag_i, diag_kwargs_i) in enumerate(zip(diag_list, diag_kwargs_list)): + for i, (diag_i, diag_kwargs_i) in enumerate( + zip(diag_list, diag_kwargs_list, strict=False) + ): diag_kwarg_filled_i = _get_default_diag_kwargs(diag_i, i) diag_kwarg_filled_i = _update(diag_kwarg_filled_i, diag_kwargs_i) diag_kwargs_filled.append(diag_kwarg_filled_i) @@ -2031,7 +2039,7 @@ def marginal_plot_with_probs_intensity( # normalize color intensity norm = Normalize(vmin=vmin, vmax=vmax) # set color intensity - for w, p in zip(weights, patches): + for w, p in zip(weights, patches, strict=False): p.set_facecolor(cmap(w)) if show_colorbar: plt.colorbar(cm.ScalarMappable(norm=norm, cmap=cmap), ax=ax_, label=label) diff --git a/sbi/diagnostics/sbc.py b/sbi/diagnostics/sbc.py index cd94d14d0..2bdf88f28 100644 --- a/sbi/diagnostics/sbc.py +++ b/sbi/diagnostics/sbc.py @@ -138,7 +138,7 @@ def _run_sbc( ranks = torch.zeros((num_sbc_samples, len(reduce_fns))) # Iterate over all sbc samples and calculate ranks. for sbc_idx, (true_theta, x_i) in tqdm( - enumerate(zip(thetas, xs)), + enumerate(zip(thetas, xs, strict=False)), total=num_sbc_samples, disable=not show_progress_bar, desc=f"Calculating ranks for {num_sbc_samples} sbc samples.", @@ -188,7 +188,7 @@ def get_nltp(thetas: Tensor, xs: Tensor, posterior: NeuralPosterior) -> Tensor: nltp = torch.zeros(thetas.shape[0]) unnormalized_log_prob = not isinstance(posterior, (DirectPosterior, ScorePosterior)) - for idx, (tho, xo) in enumerate(zip(thetas, xs)): + for idx, (tho, xo) in enumerate(zip(thetas, xs, strict=False)): # Log prob of true params under posterior. if unnormalized_log_prob: nltp[idx] = -posterior.potential(tho, x=xo) @@ -266,7 +266,7 @@ def check_prior_vs_dap(prior_samples: Tensor, dap_samples: Tensor) -> Tensor: return torch.tensor([ c2st(s1.unsqueeze(1), s2.unsqueeze(1)) - for s1, s2 in zip(prior_samples.T, dap_samples.T) + for s1, s2 in zip(prior_samples.T, dap_samples.T, strict=False) ]) diff --git a/sbi/neural_nets/factory.py b/sbi/neural_nets/factory.py index b12784067..e6d65b151 100644 --- a/sbi/neural_nets/factory.py +++ b/sbi/neural_nets/factory.py @@ -112,6 +112,7 @@ def classifier_nn( check_net_device(embedding_net_theta, "cpu", embedding_net_warn_msg), check_net_device(embedding_net_x, "cpu", embedding_net_warn_msg), ), + strict=False, ), **kwargs, ) @@ -194,6 +195,7 @@ def likelihood_nn( check_net_device(embedding_net, "cpu", embedding_net_warn_msg), num_components, ), + strict=False, ), **kwargs, ) @@ -332,6 +334,7 @@ def posterior_nn( check_net_device(embedding_net, "cpu", embedding_net_warn_msg), num_components, ), + strict=False, ), **kwargs, ) @@ -434,6 +437,7 @@ def posterior_score_nn( hidden_features, embedding_net, ), + strict=False, ), **kwargs, ) diff --git a/sbi/samplers/mcmc/slice_numpy.py b/sbi/samplers/mcmc/slice_numpy.py index 08f7f8871..b71e218b3 100644 --- a/sbi/samplers/mcmc/slice_numpy.py +++ b/sbi/samplers/mcmc/slice_numpy.py @@ -289,7 +289,7 @@ def run(self, num_samples: int) -> np.ndarray: ): all_samples: Sequence[np.ndarray] = Parallel(n_jobs=self.num_workers)( # pyright: ignore[reportAssignmentType] delayed(self.run_fun)(num_samples, initial_params_batch, seed) - for initial_params_batch, seed in zip(self.x, seeds) + for initial_params_batch, seed in zip(self.x, seeds, strict=False) ) samples = np.stack(all_samples).astype(np.float32) diff --git a/sbi/samplers/vi/vi_divergence_optimizers.py b/sbi/samplers/vi/vi_divergence_optimizers.py index 89c345b9b..be7eb1e66 100644 --- a/sbi/samplers/vi/vi_divergence_optimizers.py +++ b/sbi/samplers/vi/vi_divergence_optimizers.py @@ -200,7 +200,7 @@ def warm_up(self, num_steps: int, method: str = "prior") -> None: def update_state(self) -> None: """This updates the current state.""" - for state_para, para in zip(self.state_dict, self.q.parameters()): + for state_para, para in zip(self.state_dict, self.q.parameters(), strict=False): if torch.isfinite(para).all(): state_para.data = para.data.clone() else: @@ -213,7 +213,7 @@ def resolve_state(self, warm_up_rounds: int = 100) -> None: Args: warm_up_rounds: Number of warm_up_round one should do after failure. """ - for state_para, para in zip(self.state_dict, self.q.parameters()): + for state_para, para in zip(self.state_dict, self.q.parameters(), strict=False): para.data = state_para.data.clone().to(para.device) self._optimizer.__init__(self.q.parameters(), self.learning_rate) self.warm_up(warm_up_rounds) @@ -464,7 +464,7 @@ def generate_elbo_particles( def update_surrogate_q(self) -> None: """Updates the surrogate with new parameters.""" for param, param_surro in zip( - self.q.parameters(), self._surrogate_q.parameters() + self.q.parameters(), self._surrogate_q.parameters(), strict=False ): param_surro.data = param.data param_surro.requires_grad = False diff --git a/sbi/simulators/simutils.py b/sbi/simulators/simutils.py index cd47e51e8..abfd355cc 100644 --- a/sbi/simulators/simutils.py +++ b/sbi/simulators/simutils.py @@ -73,7 +73,7 @@ def simulator_seeded(theta: Tensor, seed) -> Tensor: ) as _: simulation_outputs: List[Tensor] = Parallel(n_jobs=num_workers)( # pyright: ignore[reportAssignmentType] delayed(simulator_seeded)(batch, batch_seed) - for batch, batch_seed in zip(batches, batch_seeds) + for batch, batch_seed in zip(batches, batch_seeds, strict=False) ) else: pbar = tqdm( diff --git a/sbi/utils/conditional_density_utils.py b/sbi/utils/conditional_density_utils.py index 829f5e1df..31d72a234 100644 --- a/sbi/utils/conditional_density_utils.py +++ b/sbi/utils/conditional_density_utils.py @@ -73,7 +73,7 @@ def _compute_covariance( # Compute E[X] * E[Y]. expected_values_of_marginals = [ _expected_value_f_of_x(prob.unsqueeze(0), lim.unsqueeze(0)) - for prob, lim in zip(_calc_marginals(probs, limits), limits) + for prob, lim in zip(_calc_marginals(probs, limits), limits, strict=False) ] return expected_value_of_joint - f(*expected_values_of_marginals) @@ -104,7 +104,7 @@ def _expected_value_f_of_x( x_values_over_which_we_integrate = [ torch.linspace(lim[0].item(), lim[1].item(), prob.shape[0], device=probs.device) - for lim, prob in zip(torch.flip(limits, [0]), probs) + for lim, prob in zip(torch.flip(limits, [0]), probs, strict=False) ] # See #403 and #404 for flip(). grids = list(torch.meshgrid(x_values_over_which_we_integrate)) expected_val = torch.sum(f(*grids) * probs) diff --git a/sbi/utils/diagnostics_utils.py b/sbi/utils/diagnostics_utils.py index aee2aa09b..4d5556183 100644 --- a/sbi/utils/diagnostics_utils.py +++ b/sbi/utils/diagnostics_utils.py @@ -75,7 +75,7 @@ def sample_fun( tqdm( Parallel(return_as="generator", n_jobs=num_workers)( delayed(sample_fun)(posterior, sample_shape, x=x, seed=s) - for x, s in zip(xs, seeds) + for x, s in zip(xs, seeds, strict=False) ), disable=not show_progress_bar, total=len(xs), diff --git a/sbi/utils/sbiutils.py b/sbi/utils/sbiutils.py index c137f3978..3090bc71a 100644 --- a/sbi/utils/sbiutils.py +++ b/sbi/utils/sbiutils.py @@ -453,7 +453,9 @@ def get_simulations_since_round( counting from 0. """ return torch.cat([ - t for t, r in zip(data, data_round_indices) if r >= starting_round_index + t + for t, r in zip(data, data_round_indices, strict=False) + if r >= starting_round_index ]) diff --git a/sbi/utils/simulation_utils.py b/sbi/utils/simulation_utils.py index b9ea9dc67..d58078ea7 100644 --- a/sbi/utils/simulation_utils.py +++ b/sbi/utils/simulation_utils.py @@ -93,7 +93,7 @@ def simulator_seeded(theta: ndarray, seed: int) -> Tensor: for xx in tqdm( Parallel(return_as="generator", n_jobs=num_workers)( delayed(simulator_seeded)(batch, seed) - for batch, seed in zip(batches, batch_seeds) + for batch, seed in zip(batches, batch_seeds, strict=False) ), total=num_simulations, disable=not show_progress_bar, diff --git a/tests/sbiutils_test.py b/tests/sbiutils_test.py index 34fd005b8..51b27c357 100644 --- a/tests/sbiutils_test.py +++ b/tests/sbiutils_test.py @@ -231,7 +231,9 @@ def __init__(self, means, preds, logits): def log_prob(self, theta): probs = zeros(theta.shape[0]) - for m, p, logit in zip(self._means, self._preds, self._logits): + for m, p, logit in zip( + self._means, self._preds, self._logits, strict=False + ): mvn = MultivariateNormal(m, p) weighted_prob = torch.exp(mvn.log_prob(theta)) * logit probs += weighted_prob diff --git a/tests/torchutils_test.py b/tests/torchutils_test.py index 028b5e8b9..10e0dff64 100644 --- a/tests/torchutils_test.py +++ b/tests/torchutils_test.py @@ -188,7 +188,7 @@ def test_dkl_gauss(): distributions.MultivariateNormal(ones(2), 0.5 * eye(2)), ) - for d1, d2 in zip(dist1, dist2): + for d1, d2 in zip(dist1, dist2, strict=False): torch_dkl = distributions.kl.kl_divergence(d1, d2) monte_carlo_dkl = kl_d_via_monte_carlo(d1, d2, num_samples=5000) diff --git a/tutorials/08_crafting_summary_statistics.ipynb b/tutorials/08_crafting_summary_statistics.ipynb index 1d7017dd7..19d5bf436 100644 --- a/tutorials/08_crafting_summary_statistics.ipynb +++ b/tutorials/08_crafting_summary_statistics.ipynb @@ -361,8 +361,8 @@ "source": [ "fig, axes = pairplot(\n", " theta_p,\n", - " limits=list(zip(prior_min, prior_max)),\n", - " ticks=list(zip(prior_min, prior_max)),\n", + " limits=list(zip(prior_min, prior_max, strict=False)),\n", + " ticks=list(zip(prior_min, prior_max, strict=False)),\n", " figsize=(7, 7),\n", " labels=[\"a\", \"b\", \"c\"],\n", " fig_kwargs=dict(\n", @@ -467,8 +467,8 @@ "\n", "fig, axes = pairplot(\n", " theta_p,\n", - " limits=list(zip(prior_min, prior_max)),\n", - " ticks=list(zip(prior_min, prior_max)),\n", + " limits=list(zip(prior_min, prior_max, strict=False)),\n", + " ticks=list(zip(prior_min, prior_max, strict=False)),\n", " figsize=(7, 7),\n", " labels=[\"a\", \"b\", \"c\"],\n", " fig_kwargs=dict(\n", diff --git a/tutorials/11_diagnostics_simulation_based_calibration.ipynb b/tutorials/11_diagnostics_simulation_based_calibration.ipynb index c54f0aa9c..54596b965 100644 --- a/tutorials/11_diagnostics_simulation_based_calibration.ipynb +++ b/tutorials/11_diagnostics_simulation_based_calibration.ipynb @@ -244,7 +244,7 @@ "fig, ax = pairplot(\n", " samples=posterior_predictive_samples,\n", " points=x_o,\n", - " limits=list(zip(x_o.flatten() - 1.0, x_o.flatten() + 1.0)),\n", + " limits=list(zip(x_o.flatten() - 1.0, x_o.flatten() + 1.0, strict=False)),\n", " upper=\"kde\",\n", " diag=\"kde\",\n", " figsize=(5, 5),\n", diff --git a/tutorials/12_iid_data_and_permutation_invariant_embeddings.ipynb b/tutorials/12_iid_data_and_permutation_invariant_embeddings.ipynb index d208180b6..aeabe880f 100644 --- a/tutorials/12_iid_data_and_permutation_invariant_embeddings.ipynb +++ b/tutorials/12_iid_data_and_permutation_invariant_embeddings.ipynb @@ -312,7 +312,7 @@ "source": [ "cs = [\n", " c2st(s1, s2)\n", - " for s1, s2 in zip(true_samples, nle_samples)\n", + " for s1, s2 in zip(true_samples, nle_samples, strict=False)\n", "]\n", "\n", "for _ in range(len(num_trials)):\n", @@ -475,7 +475,7 @@ " xoi[0, : len(xo), :] = xo\n", " npe_samples.append(posterior.sample(sample_shape=(num_samples,), x=xoi))\n", "\n", - "cs = [c2st(s1, s2) for s1, s2 in zip(true_samples, npe_samples)]\n", + "cs = [c2st(s1, s2) for s1, s2 in zip(true_samples, npe_samples, strict=False)]\n", "\n", "for _ in range(len(num_trials)):\n", " print(f\"c2st score for num_trials={num_trials[_]}: {cs[_].item():.2f}\")" From d6aa95fdecbc243cb2d59594c6dc338f9e625f7f Mon Sep 17 00:00:00 2001 From: Jan Date: Wed, 26 Feb 2025 14:51:17 +0100 Subject: [PATCH 03/17] remove uv lock, update docs action --- .github/workflows/build_docs.yml | 27 +- uv.lock | 3540 ------------------------------ 2 files changed, 10 insertions(+), 3557 deletions(-) delete mode 100644 uv.lock diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index 7e1e58991..5b748aee3 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -17,31 +17,24 @@ jobs: fetch-depth: 0 lfs: false - - name: Set up Python - uses: actions/setup-python@v2 + - name: Install uv and set the python version + uses: astral-sh/setup-uv@v5 with: python-version: '3.10' + enable-cache: true + cache-dependency-glob: "pyproject.toml" - - name: Cache dependency - id: cache-dependencies - uses: actions/cache@v4 - with: - path: ~/.cache/pip - key: ${{ runner.os }}-pip - - - name: Install sbi and dependencies - run: | - python -m pip install --upgrade pip - python -m pip install .[doc] + - name: Install dependencies with uv + run: uv sync --all-extras --doc - name: strip output except plots and prints from tutorial notebooks run: | - python tests/strip_notebook_outputs.py tutorials/ + uv run python tests/strip_notebook_outputs.py tutorials/ - name: convert notebooks to markdown run: | cd docs - jupyter nbconvert --to markdown ../tutorials/*.ipynb --output-dir docs/tutorials/ + uv run jupyter nbconvert --to markdown ../tutorials/*.ipynb --output-dir docs/tutorials/ - name: Configure Git user for bot run: | @@ -52,10 +45,10 @@ jobs: if: ${{ github.event_name == 'push' }} run: | cd docs - 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"pymc>=5.21.0", + "pymc>=5.0.0", "zuko>=1.2.0", ] From 4e8a07d268ad33b5b14023fe62cb095fb94d2420 Mon Sep 17 00:00:00 2001 From: Jan Date: Wed, 26 Feb 2025 15:01:22 +0100 Subject: [PATCH 05/17] fix workflows --- .github/workflows/build_docs.yml | 1 + .github/workflows/lint.yml | 1 + .github/workflows/publish.yml | 6 +++--- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml index 5b748aee3..aad626f28 100644 --- a/.github/workflows/build_docs.yml +++ b/.github/workflows/build_docs.yml @@ -5,6 +5,7 @@ on: - main release: types: [ published ] + workflow_dispatch: jobs: docs: diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 50d1d2ced..2ab03f281 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -42,6 +42,7 @@ jobs: with: python-version: '3.10' enable-cache: true + cache-dependency-glob: "pyproject.toml" - name: Install dependencies with uv run: uv sync --all-extras --dev diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml index 1d390387f..961b12e4d 100644 --- a/.github/workflows/publish.yml +++ b/.github/workflows/publish.yml @@ -25,7 +25,7 @@ jobs: - name: Build a binary wheel and a source tarball run: python3 -m build - name: Store the distribution packages - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: python-package-distributions path: dist/ @@ -45,7 +45,7 @@ jobs: steps: - name: Download all the dists - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: python-package-distributions path: dist/ @@ -66,7 +66,7 @@ jobs: steps: - name: Download all the dists - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: python-package-distributions path: dist/ From a555dd3788628a03149307ce504dcbe363353981 Mon Sep 17 00:00:00 2001 From: Jan Date: Tue, 4 Mar 2025 06:51:27 +0100 Subject: [PATCH 06/17] fix pymc x-failing tests --- tests/mcmc_test.py | 4 ++-- tests/posterior_sampler_test.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/mcmc_test.py b/tests/mcmc_test.py index 0308e31d8..4a451e419 100644 --- a/tests/mcmc_test.py +++ b/tests/mcmc_test.py @@ -188,8 +188,8 @@ def lp_f(x, track_gradients=True): pytest.param( "nuts_pymc", marks=pytest.mark.xfail( - condition=sys.version_info >= (3, 12), - reason="Fails with pymc 5.20.1", + condition=sys.version_info >= (3, 10), + reason="Fails with pymc>=5.20.1 and python>=3.10", strict=True, raises=TypeError, ), diff --git a/tests/posterior_sampler_test.py b/tests/posterior_sampler_test.py index a0236df88..f9ed5430e 100644 --- a/tests/posterior_sampler_test.py +++ b/tests/posterior_sampler_test.py @@ -30,8 +30,8 @@ pytest.param( "nuts_pymc", marks=pytest.mark.xfail( - condition=sys.version_info >= (3, 12), - reason="Fails with pymc 5.20.1", + condition=sys.version_info >= (3, 10), + reason="Fails with pymc>=5.20.1 and python>=3.10", raises=TypeError, ), ), From 0e45d3631783f385c9dc2dd4805277790a39bc3c Mon Sep 17 00:00:00 2001 From: Jan Date: Tue, 4 Mar 2025 08:52:33 +0100 Subject: [PATCH 07/17] fix python 3.13 induced errors --- pyproject.toml | 4 ++-- tests/circular_import_test.py | 2 +- tests/vi_test.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 4f57b1665..e16e209d9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,14 +33,14 @@ dependencies = [ "joblib>=1.0.0", "matplotlib", "notebook <= 6.4.12", - "numpy<2.0.0", + "numpy", "pillow", "pyknos>=0.16.0", "pyro-ppl>=1.3.1", "scikit-learn", "scipy", "tensorboard", - "torch>=1.13.0, <2.6.0", + "torch>=1.13.0", "tqdm", "pymc>=5.0.0", "zuko>=1.2.0", diff --git a/tests/circular_import_test.py b/tests/circular_import_test.py index 202652f0e..99ce89e42 100644 --- a/tests/circular_import_test.py +++ b/tests/circular_import_test.py @@ -96,7 +96,7 @@ def test_for_circular_imports(): import_first_function(module.__name__) del module - except ImportError as e: + except (ImportError, NameError) as e: # NOTE: There might be other errors which are intended if "circular import" in str(e): # This is a circular import detected diff --git a/tests/vi_test.py b/tests/vi_test.py index ca26fa559..2ef0e0073 100644 --- a/tests/vi_test.py +++ b/tests/vi_test.py @@ -261,7 +261,7 @@ def test_pickle_support(q: str): with tempfile.NamedTemporaryFile(suffix=".pt") as f: torch.save(posterior, f.name) - posterior_loaded = torch.load(f.name) + posterior_loaded = torch.load(f.name, weights_only=False) assert (posterior._x == posterior_loaded._x).all(), ( "Mhh, something with the pickled is strange" ) From f0ab7d2cf391af742eace55e172539b2540db754 Mon Sep 17 00:00:00 2001 From: Jan Date: Tue, 4 Mar 2025 09:09:39 +0100 Subject: [PATCH 08/17] fix torch deps and plot pyright --- pyproject.toml | 2 +- sbi/analysis/plot.py | 12 +++++++++--- 2 files changed, 10 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e16e209d9..e7100807e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -40,7 +40,7 @@ dependencies = [ "scikit-learn", "scipy", "tensorboard", - "torch>=1.13.0", + "torch>=1.13.0, <2.6.0", "tqdm", "pymc>=5.0.0", "zuko>=1.2.0", diff --git a/sbi/analysis/plot.py b/sbi/analysis/plot.py index e443e57d0..e90a5a15d 100644 --- a/sbi/analysis/plot.py +++ b/sbi/analysis/plot.py @@ -124,12 +124,18 @@ def plt_hist_2d( ax: Axes, samples_col: np.ndarray, samples_row: np.ndarray, - limits_col: torch.Tensor, - limits_row: torch.Tensor, + limits_col: Union[torch.Tensor, List], + limits_row: Union[torch.Tensor, List], offdiag_kwargs: Dict, ): - hist_kwargs = copy.deepcopy(offdiag_kwargs) """Plot 2D histogram.""" + hist_kwargs = copy.deepcopy(offdiag_kwargs) + + if isinstance(limits_col, torch.Tensor): + limits_col = limits_col.tolist() + if isinstance(limits_row, torch.Tensor): + limits_row = limits_row.tolist() + if ( "bins" not in hist_kwargs["np_hist_kwargs"] or hist_kwargs["np_hist_kwargs"]["bins"] is None From 3c83d038766c9ae73a6f16ec4d8a4d9550d67e06 Mon Sep 17 00:00:00 2001 From: manuelgloeckler Date: Tue, 4 Mar 2025 11:29:20 +0100 Subject: [PATCH 09/17] Fix circular import test --- tests/circular_import_test.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/tests/circular_import_test.py b/tests/circular_import_test.py index 99ce89e42..5338c3799 100644 --- a/tests/circular_import_test.py +++ b/tests/circular_import_test.py @@ -22,9 +22,8 @@ def import_first_function(module_name: str): if functions: first_function_name, first_function = functions[0] cmd = f"from {module_name} import {first_function_name}" + cmd += f"; del {first_function_name}" exec(cmd) - cmd_del = f"del {first_function_name}" - exec(cmd_del) else: pass @@ -96,11 +95,15 @@ def test_for_circular_imports(): import_first_function(module.__name__) del module - except (ImportError, NameError) as e: + except ImportError as e: # NOTE: There might be other errors which are intended if "circular import" in str(e): # This is a circular import detected errors.append(f"Circular import detected in {module_name}. Error: {e}") print(f"Circular import detected in {module_name}") + except Exception as e: + # NOTE: There might be other errors which we catch here and report + print(f"Error in {module_name}: {e}") + errors.append(f"Error in {module_name}: {e}") assert len(errors) == 0, "\n".join(errors) From 0c61e358ccad4279ad66f8322128cf6ecda3e596 Mon Sep 17 00:00:00 2001 From: Jan Date: Thu, 6 Mar 2025 10:28:24 +0100 Subject: [PATCH 10/17] test more python versions --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cacffc98d..5d396c8ba 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,7 +20,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.10', '3.13'] + python-version: ['3.10', '3.11', '3.12', '3.13'] steps: - name: Checkout From d51e9fbcb7892ef65f796c233f5c0a0dcc1408f0 Mon Sep 17 00:00:00 2001 From: Jan Date: Thu, 6 Mar 2025 10:38:08 +0100 Subject: [PATCH 11/17] add numfocus badge and credits in readme --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index f209b33aa..c3ccb5929 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,7 @@ [![codecov](https://codecov.io/gh/sbi-dev/sbi/branch/main/graph/badge.svg)](https://codecov.io/gh/sbi-dev/sbi) [![GitHub license](https://img.shields.io/github/license/sbi-dev/sbi)](https://github.com/sbi-dev/sbi/blob/master/LICENSE.txt) [![DOI](https://joss.theoj.org/papers/10.21105/joss.02505/status.svg)](https://doi.org/10.21105/joss.02505) +[![NumFOCUS affiliated](https://camo.githubusercontent.com/a0f197cee66ccd8ed498cf64e9f3f384c78a072fe1e65bada8d3015356ac7599/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f4e756d464f4355532d616666696c696174656425323070726f6a6563742d6f72616e67652e7376673f7374796c653d666c617426636f6c6f72413d45313532334426636f6c6f72423d303037443841)] ## `sbi`: Simulation-Based Inference @@ -205,7 +206,7 @@ Durkan's `lfi`. `sbi` runs as a community project. See also `sbi` has been supported by the German Federal Ministry of Education and Research (BMBF) through project ADIMEM (FKZ 01IS18052 A-D), project SiMaLeSAM (FKZ 01IS21055A) and the Tübingen AI Center (FKZ 01IS18039A). Since 2024, `sbi` is supported by the appliedAI -Institute for Europe. +Institute for Europe, and by NumFOCUS. ## License From cb1129486bfd2a8e3a6f476adc5ea41a02e767c4 Mon Sep 17 00:00:00 2001 From: Jan Date: Thu, 6 Mar 2025 11:00:28 +0100 Subject: [PATCH 12/17] remove testmon temporarily --- .github/workflows/ci.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5d396c8ba..e150647b3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,16 +49,16 @@ jobs: restore-keys: | uv-${{ runner.os }}-${{ matrix.python-version }}- - - name: Cache testmon data - uses: actions/cache@v4 - with: - path: .testmondata - key: testmon-${{ runner.os }}-${{ matrix.python-version }}-${{ github.ref }} - restore-keys: | - testmon-${{ runner.os }}-${{ matrix.python-version }}- + # - name: Cache testmon data + # uses: actions/cache@v4 + # with: + # path: .testmondata + # key: testmon-${{ runner.os }}-${{ matrix.python-version }}-${{ github.ref }} + # restore-keys: | + # testmon-${{ runner.os }}-${{ matrix.python-version }}- - name: Run the fast CPU tests with coverage - run: uv run pytest --testmon-forceselect -v -n auto -m "not slow and not gpu" --cov=sbi --cov-report=xml tests/ + run: uv run pytest -v -n auto -m "not slow and not gpu" --cov=sbi --cov-report=xml tests/ - name: Upload coverage to Codecov uses: codecov/codecov-action@v4 From 420993989a7fa159a78c1ac420d7cd0d2eb12830 Mon Sep 17 00:00:00 2001 From: Jan Date: Thu, 6 Mar 2025 12:44:03 +0100 Subject: [PATCH 13/17] add testmon adain --- .github/workflows/ci.yml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e150647b3..5d396c8ba 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,16 +49,16 @@ jobs: restore-keys: | uv-${{ runner.os }}-${{ matrix.python-version }}- - # - name: Cache testmon data - # uses: actions/cache@v4 - # with: - # path: .testmondata - # key: testmon-${{ runner.os }}-${{ matrix.python-version }}-${{ github.ref }} - # restore-keys: | - # testmon-${{ runner.os }}-${{ matrix.python-version }}- + - name: Cache testmon data + uses: actions/cache@v4 + with: + path: .testmondata + key: testmon-${{ runner.os }}-${{ matrix.python-version }}-${{ github.ref }} + restore-keys: | + testmon-${{ runner.os }}-${{ matrix.python-version }}- - name: Run the fast CPU tests with coverage - run: uv run pytest -v -n auto -m "not slow and not gpu" --cov=sbi --cov-report=xml tests/ + run: uv run pytest --testmon-forceselect -v -n auto -m "not slow and not gpu" --cov=sbi --cov-report=xml tests/ - name: Upload coverage to Codecov uses: codecov/codecov-action@v4 From ac83fabfb888b7cc877d59ba3a88abb01237d386 Mon Sep 17 00:00:00 2001 From: Jan Date: Thu, 6 Mar 2025 15:05:08 +0100 Subject: [PATCH 14/17] test python version in CD --- .github/workflows/cd.yml | 5 ++++- .github/workflows/ci.yml | 8 ++++---- .github/workflows/lint.yml | 2 +- 3 files changed, 9 insertions(+), 6 deletions(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 53ef0845e..c4566c42b 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -17,6 +17,9 @@ jobs: cd: name: Continuous Deployment runs-on: ubuntu-latest + strategy: + matrix: + python-version: ['3.10', '3.11', '3.12', '3.13'] steps: - name: Checkout @@ -28,7 +31,7 @@ jobs: - name: Install uv and set the python version uses: astral-sh/setup-uv@v5 with: - python-version: '3.10' + python-version: ${{ matrix.python-version }} enable-cache: true cache-dependency-glob: "pyproject.toml" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5d396c8ba..368f136a5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,4 +1,4 @@ -name: Tests +name: Continuous Integration on: [pull_request, workflow_dispatch] @@ -12,7 +12,7 @@ concurrency: jobs: ci: - name: CI + name: Continuous Integration runs-on: ubuntu-latest if: | github.event_name == 'push' || @@ -20,7 +20,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.10', '3.11', '3.12', '3.13'] + python-version: ['3.10'] steps: - name: Checkout @@ -57,7 +57,7 @@ jobs: restore-keys: | testmon-${{ runner.os }}-${{ matrix.python-version }}- - - name: Run the fast CPU tests with coverage + - name: Run fast CPU tests with coverage run: uv run pytest --testmon-forceselect -v -n auto -m "not slow and not gpu" --cov=sbi --cov-report=xml tests/ - name: Upload coverage to Codecov diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 2ab03f281..b9e8fbf4a 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -28,7 +28,7 @@ jobs: extra_args: --all-files --show-diff-on-failure pyright: - name: Check types + name: type checking. runs-on: ubuntu-latest steps: - name: Checkout From 702351f5f33aa441b02d1655f2eccba546c902f6 Mon Sep 17 00:00:00 2001 From: Jan Date: Thu, 6 Mar 2025 18:05:17 +0100 Subject: [PATCH 15/17] change locally passing but ci failing test --- tests/lc2st_test.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/tests/lc2st_test.py b/tests/lc2st_test.py index 62f5e633b..816aa3772 100644 --- a/tests/lc2st_test.py +++ b/tests/lc2st_test.py @@ -189,7 +189,7 @@ def test_lc2st_true_positiv_rate(method): @pytest.mark.slow @pytest.mark.parametrize("method", (LC2ST, LC2ST_NF)) -def test_lc2st_false_positiv_rate(method): +def test_lc2st_false_positiv_rate(method, set_seed): """Tests the false positiv rate of the LC2ST-(NF) test: for a "good" estimator, the LC2ST-(NF) should not reject the null hypothesis.""" num_runs = 100 @@ -198,7 +198,6 @@ def test_lc2st_false_positiv_rate(method): # use big num_train and num_epochs to obtain "good" estimator # (convergence of the estimator) num_train = 5_000 - num_epochs = 200 num_cal = 1_000 num_eval = 10_000 @@ -215,7 +214,7 @@ def test_lc2st_false_positiv_rate(method): # Train the neural posterior estimators inference = NPE(prior, density_estimator='maf') inference = inference.append_simulations(theta=theta_train, x=x_train) - npe = inference.train(training_batch_size=100, max_num_epochs=num_epochs) + npe = inference.train(training_batch_size=100) thetas = prior.sample((num_cal,)) xs = simulator(thetas) From 0ccb616d5d8b8f5c0f66c47b4282d1ed7e786d1a Mon Sep 17 00:00:00 2001 From: Jan Date: Fri, 7 Mar 2025 14:51:47 +0100 Subject: [PATCH 16/17] turn off fast fail --- .github/workflows/cd.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index c4566c42b..723b85db6 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -18,6 +18,7 @@ jobs: name: Continuous Deployment runs-on: ubuntu-latest strategy: + fail-fast: false matrix: python-version: ['3.10', '3.11', '3.12', '3.13'] From bc2dbbdac959b4d816d9083473d32d59ecd15c56 Mon Sep 17 00:00:00 2001 From: Jan Date: Fri, 7 Mar 2025 16:02:34 +0100 Subject: [PATCH 17/17] remote test still failing, increas n --- tests/lc2st_test.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/lc2st_test.py b/tests/lc2st_test.py index 816aa3772..529ca7f2a 100644 --- a/tests/lc2st_test.py +++ b/tests/lc2st_test.py @@ -197,7 +197,7 @@ def test_lc2st_false_positiv_rate(method, set_seed): # use big num_train and num_epochs to obtain "good" estimator # (convergence of the estimator) - num_train = 5_000 + num_train = 10_000 num_cal = 1_000 num_eval = 10_000