Maintain project requirements and code QA (#268)

- Apply ruff 0.9.3 - explicitly install R in GHA tests - explicitly install torch along with pgmpy - Remove reliance on ananke, since it has way too strict version pins (poetry strikes again)
y0-causal-inference · Jan 24, 2025 · da2032c · da2032c
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -64,6 +64,8 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: ${{ matrix.python-version }}
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
       - name: Install dependencies
         run: |
           pip install tox tox-uv

diff --git a/notebooks/Make Counterfactual Graph.ipynb b/notebooks/Make Counterfactual Graph.ipynb
@@ -358,9 +358,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert (\n",
-    "    figure_11a_calculated == figure_11a.graph\n",
-    "), \"Calculated figure 11a is not equal to the actual figure 11a\"\n",
+    "assert figure_11a_calculated == figure_11a.graph, (\n",
+    "    \"Calculated figure 11a is not equal to the actual figure 11a\"\n",
+    ")\n",
     "print(\"Figure 11a calculated is correct\")"
    ]
   },
@@ -465,9 +465,9 @@
    },
    "outputs": [],
    "source": [
-    "assert (\n",
-    "    figure_11b_calculated == figure_11b.graph\n",
-    "), \"Calculated figure 11b is not equal to the actual figure 11b\"\n",
+    "assert figure_11b_calculated == figure_11b.graph, (\n",
+    "    \"Calculated figure 11b is not equal to the actual figure 11b\"\n",
+    ")\n",
     "\n",
     "print(\"Figure 11b calculated is correct\")"
    ]
@@ -523,9 +523,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert (\n",
-    "    figure_11c_calculated == figure_11c.graph\n",
-    "), \"Calculated figure 11c is not equal to the actual figure 11c\"\n",
+    "assert figure_11c_calculated == figure_11c.graph, (\n",
+    "    \"Calculated figure 11c is not equal to the actual figure 11c\"\n",
+    ")\n",
     "\n",
     "print(\"Figure 11c calculated is correct\")"
    ]
@@ -586,9 +586,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "assert (\n",
-    "    figure_9c_calculated == figure_9c.graph\n",
-    "), \"Calculated figure 9c is not equal to the actual figure 9c\"\n",
+    "assert figure_9c_calculated == figure_9c.graph, (\n",
+    "    \"Calculated figure 9c is not equal to the actual figure 9c\"\n",
+    ")\n",
     "print(\"Figure 9c calculated is correct\")"
    ]
   },
@@ -728,7 +728,7 @@
    "source": [
     "for c_component in C_components:\n",
     "    print(\n",
-    "        f\"C-Component:{c_component} Interventions: {get_events_of_district(cf_graph,c_component,new_event)}\"\n",
+    "        f\"C-Component:{c_component} Interventions: {get_events_of_district(cf_graph, c_component, new_event)}\"\n",
     "    )"
    ]
   },

diff --git a/pyproject.toml b/pyproject.toml
@@ -74,8 +74,9 @@ r = [
 tests = [
     "pytest",
     "coverage",
-    "ananke-causal",
+    # "ananke-causal",
     "pgmpy",
+    "torch",
 ]
 docs = [
     # waiting on https://github.com/readthedocs/sphinx_rtd_theme/issues/1582

diff --git a/src/y0/algorithm/conditional_independencies.py b/src/y0/algorithm/conditional_independencies.py
@@ -21,11 +21,11 @@
 from ..util.combinatorics import powerset
 
 __all__ = [
+    "add_ci_undirected_edges",
     "are_d_separated",
-    "minimal",
     "get_conditional_independencies",
+    "minimal",
     "test_conditional_independencies",
-    "add_ci_undirected_edges",
 ]
 
 

diff --git a/src/y0/algorithm/counterfactual_transport/__init__.py b/src/y0/algorithm/counterfactual_transport/__init__.py
@@ -15,13 +15,12 @@
 )
 
 __all__ = [
-    "unconditional_cft",
-    "conditional_cft",
-    "transport_unconditional_counterfactual_query",
-    "transport_conditional_counterfactual_query",
-    #
-    "Event",
     "CFTDomain",
     "ConditionalCFTResult",
+    "Event",
     "UnconditionalCFTResult",
+    "conditional_cft",
+    "transport_conditional_counterfactual_query",
+    "transport_unconditional_counterfactual_query",
+    "unconditional_cft",
 ]
diff --git a/src/y0/algorithm/counterfactual_transport/ancestor_utils.py b/src/y0/algorithm/counterfactual_transport/ancestor_utils.py
@@ -10,8 +10,8 @@
 
 __all__ = [
     "get_ancestors_of_counterfactual",
-    "minimize_counterfactual",
     "get_ancestral_components",
+    "minimize_counterfactual",
 ]
 
 logger = logging.getLogger(__file__)

diff --git a/src/y0/algorithm/counterfactual_transport/api.py b/src/y0/algorithm/counterfactual_transport/api.py
@@ -41,26 +41,24 @@
 )
 
 __all__ = [
-    # TODO do a proper audit of which of these a user should ever have to import
-    "unconditional_cft",
-    "conditional_cft",
-    "transport_unconditional_counterfactual_query",
-    "transport_conditional_counterfactual_query",
-    #
-    "Event",
     "CFTDomain",
     "ConditionalCFTResult",
+    "Event",
     "UnconditionalCFTResult",
-    # Utilities
-    "simplify",
-    "minimize_event",
-    "same_district",
-    "is_counterfactual_factor_form",
-    "get_counterfactual_factors",
+    "conditional_cft",
     "convert_to_counterfactual_factor_form",
-    "do_counterfactual_factor_factorization",
     "counterfactual_factors_are_transportable",
+    "do_counterfactual_factor_factorization",
+    "get_counterfactual_factors",
+    "is_counterfactual_factor_form",
+    "minimize_event",
+    "same_district",
+    "simplify",
+    "transport_conditional_counterfactual_query",
     "transport_district_intervening_on_parents",
+    "transport_unconditional_counterfactual_query",
+    "unconditional_cft",
+    # TODO do a proper audit of which of these a user should ever have to import
     # TODO add functions/classes/variables you want to appear in the docs and be exposed to the user in this list
     #  Run tox -e docs then `open docs/build/html/index.html` to see docs
 ]

diff --git a/src/y0/algorithm/estimation/__init__.py b/src/y0/algorithm/estimation/__init__.py
@@ -17,8 +17,8 @@
 )
 
 __all__ = [
-    "estimate_ace",
     "df_covers_graph",
+    "estimate_ace",
 ]
 
 

diff --git a/src/y0/algorithm/estimation/estimators.py b/src/y0/algorithm/estimation/estimators.py
@@ -12,9 +12,9 @@
 from y0.graph import NxMixedGraph, get_district_and_predecessors, is_p_fixable
 
 __all__ = [
+    "get_beta_primal",
     "get_primal_ipw_ace",
     "get_primal_ipw_point_estimate",
-    "get_beta_primal",
 ]
 
 #: The list of Ananke estimators implemented in

diff --git a/src/y0/algorithm/estimation/linear_scm.py b/src/y0/algorithm/estimation/linear_scm.py
@@ -11,9 +11,9 @@
 from y0.graph import NxMixedGraph, sympy_nested
 
 __all__ = [
-    "get_single_door",
     "evaluate_admg",
     "evaluate_lscm",
+    "get_single_door",
 ]
 
 EvalRv = dict[sympy.Symbol, sympy.core.numbers.Rational]

diff --git a/src/y0/algorithm/falsification.py b/src/y0/algorithm/falsification.py
@@ -15,9 +15,9 @@
 from ..struct import CITest, DSeparationJudgement, _ensure_method
 
 __all__ = [
-    "get_graph_falsifications",
-    "get_falsifications",
     "Falsifications",
+    "get_falsifications",
+    "get_graph_falsifications",
 ]
 
 

diff --git a/src/y0/algorithm/identify/__init__.py b/src/y0/algorithm/identify/__init__.py
@@ -58,15 +58,12 @@
 from .utils import Identification, Query, Unidentifiable
 
 __all__ = [
-    # Algorithms
-    "identify_outcomes",
-    "identify",
+    "Identification",
+    "Query",
+    "Unidentifiable",
     "id_star",
     "idc",
     "idc_star",
-    # Data Structures
-    "Query",
-    # Exceptions
-    "Unidentifiable",
-    "Identification",
+    "identify",
+    "identify_outcomes",
 ]
diff --git a/src/y0/algorithm/identify/cg.py b/src/y0/algorithm/identify/cg.py
@@ -14,13 +14,13 @@
 from y0.graph import NxMixedGraph
 
 __all__ = [
-    "has_same_function",
     "extract_interventions",
+    "has_same_function",
+    "is_not_self_intervened",
     "is_pw_equivalent",
-    "merge_pw",
     "make_counterfactual_graph",
     "make_parallel_worlds_graph",
-    "is_not_self_intervened",
+    "merge_pw",
 ]
 
 

diff --git a/src/y0/algorithm/identify/utils.py b/src/y0/algorithm/identify/utils.py
@@ -20,8 +20,8 @@
 from y0.mutate.canonicalize_expr import canonical_expr_equal
 
 __all__ = [
-    "Query",
     "Identification",
+    "Query",
     "Unidentifiable",
     "str_nodes_to_variable_nodes",
 ]

diff --git a/src/y0/algorithm/separation/sigma_separation.py b/src/y0/algorithm/separation/sigma_separation.py
@@ -11,8 +11,8 @@
 
 __all__ = [
     "are_sigma_separated",
-    "is_z_sigma_open",
     "get_equivalence_classes",
+    "is_z_sigma_open",
 ]
 
 

diff --git a/src/y0/algorithm/simplify_latent.py b/src/y0/algorithm/simplify_latent.py
@@ -15,13 +15,13 @@
 from ..graph import DEFAULT_TAG, NxMixedGraph, _ensure_set
 
 __all__ = [
-    "evans_simplify",
-    "simplify_latent_dag",
     "SimplifyResults",
-    "remove_widow_latents",
-    "transform_latents_with_parents",
+    "evans_simplify",
     "remove_redundant_latents",
     "remove_unidirectional_latents",
+    "remove_widow_latents",
+    "simplify_latent_dag",
+    "transform_latents_with_parents",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/y0/algorithm/taheri_design.py b/src/y0/algorithm/taheri_design.py
@@ -26,10 +26,10 @@
 from y0.util.combinatorics import powerset
 
 __all__ = [
-    "taheri_design_admg",
-    "taheri_design_dag",
     "Result",
     "draw_results",
+    "taheri_design_admg",
+    "taheri_design_dag",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/y0/algorithm/tian_id.py b/src/y0/algorithm/tian_id.py
@@ -23,12 +23,12 @@
 from y0.graph import NxMixedGraph
 
 __all__ = [
-    "identify_district_variables",
+    "compute_ancestral_set_q_value",
+    "compute_c_factor",
     "compute_c_factor_conditioning_on_topological_predecessors",
-    "compute_q_value_of_variables_with_low_topological_ordering_indices",
     "compute_c_factor_marginalizing_over_topological_successors",
-    "compute_c_factor",
-    "compute_ancestral_set_q_value",
+    "compute_q_value_of_variables_with_low_topological_ordering_indices",
+    "identify_district_variables",
 ]
 
 logger = logging.getLogger(__name__)

diff --git a/src/y0/algorithm/transport.py b/src/y0/algorithm/transport.py
@@ -28,9 +28,9 @@
 from y0.mutate.canonicalize_expr import canonicalize
 
 __all__ = [
+    "TransportQuery",
     "identify_target_outcomes",
     "trso",
-    "TransportQuery",
 ]
 
 logger = logging.getLogger(__name__)