format with black

pph-collective · Feb 15, 2023 · a27b361 · a27b361
1 parent 080a8d4
commit a27b361
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Showing 25 changed files with 45 additions and 95 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -19,7 +19,7 @@ nanoid = "^2.0"
 numpy = "^1.23"
 black = {version = "^23.1.0", optional = true}
 flake8 = {version = "^3.8", optional = true}
-mypy = {version = "^0.812", optional = true}
+mypy = {version = "^1.0.0", optional = true}
 mkdocs = {version = "^1.1", optional = true}
 mkdocs-material = {version = "^7.0", optional = true}
 mkdocstrings = {version = "^0.15.0", optional = true}

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -9,6 +9,7 @@
 from titan.agent import Agent, Relationship
 from titan.location import Location
 
+
 # helper method to generate a fake number deterministically
 class FakeRandom:
     def __init__(self, num: float, fake_choice: int = 0):

diff --git a/tests/exposures/knowledge_test.py b/tests/exposures/knowledge_test.py
@@ -89,7 +89,6 @@ def test_knowledge_influence(make_model, make_agent):
 
 @pytest.mark.unit
 def test_knowledge_exposure(make_model, make_agent, params):
-
     # test update all agents for knowledge
     params.exposures.knowledge = True
     params.knowledge.prob = 0.0

diff --git a/tests/integration_test.py b/tests/integration_test.py
@@ -13,6 +13,7 @@
 from titan.model import TITAN
 from titan.run_titan import script_init
 
+
 # overwrite
 @pytest.fixture
 def params_integration(tmpdir):

diff --git a/titan/exposures/base_exposure.py b/titan/exposures/base_exposure.py
@@ -6,7 +6,6 @@
 
 
 class BaseExposure:
-
     name: str = ""
     """Name of exposure in the params file.  Also used to name the attribute in Agent"""
 

diff --git a/titan/exposures/hiv.py b/titan/exposures/hiv.py
@@ -8,7 +8,6 @@
 
 
 class HIV(base_exposure.BaseExposure):
-
     name: str = "hiv"
     stats: List[str] = ["hiv", "hiv_dx", "hiv_aids", "hiv_new", "hiv_dx_new"]
     """

diff --git a/titan/exposures/knowledge.py b/titan/exposures/knowledge.py
@@ -11,7 +11,6 @@
 
 
 class Knowledge(base_exposure.BaseExposure):
-
     name: str = "knowledge"
     stats: List[str] = ["knowledge_aware"]
     """

diff --git a/titan/exposures/monkeypox.py b/titan/exposures/monkeypox.py
@@ -8,7 +8,6 @@
 
 
 class MonkeyPox(base_exposure.BaseExposure):
-
     name: str = "monkeypox"
     stats: List[str] = [
         "monkeypox",

diff --git a/titan/features/external_exposure.py b/titan/features/external_exposure.py
@@ -5,7 +5,6 @@
 
 
 class ExternalExposure(base_feature.BaseFeature):
-
     name = "external_exposure"
 
     def __init__(self, agent: "agent.Agent"):

diff --git a/titan/features/high_risk.py b/titan/features/high_risk.py
@@ -11,7 +11,6 @@
 
 
 class HighRisk(base_feature.BaseFeature):
-
     name = "high_risk"
     stats = [
         "high_risk_new",
@@ -76,7 +75,6 @@ def update_agent(self, model: "model.TITAN"):
 
             # incarcerated last step, evaluate agent's partners for high risk
             elif self.agent.incar.time == model.time - 1:  # type: ignore[attr-defined]
-
                 # put partners in high risk
                 for partner in self.agent.get_partners(
                     self.agent.location.params.high_risk.partnership_types

diff --git a/titan/features/incar.py b/titan/features/incar.py
@@ -8,7 +8,6 @@
 
 
 class Incar(base_feature.BaseFeature):
-
     name = "incar"
     stats = ["incar", "incar_hiv", "new_release", "new_release_hiv"]
     """

diff --git a/titan/features/partner_tracing.py b/titan/features/partner_tracing.py
@@ -4,7 +4,6 @@
 
 
 class PartnerTracing(base_feature.BaseFeature):
-
     name = "partner_tracing"
 
     def __init__(self, agent: "agent.Agent"):

diff --git a/titan/features/prep.py b/titan/features/prep.py
@@ -11,7 +11,6 @@
 
 
 class Prep(base_feature.BaseFeature):
-
     name = "prep"
     stats = ["prep", "prep_new", "prep_injectable", "prep_oral"]
     """

diff --git a/titan/features/random_trial.py b/titan/features/random_trial.py
@@ -9,7 +9,6 @@
 
 
 class RandomTrial(base_feature.BaseFeature):
-
     name = "random_trial"
     stats = [
         "random_trial",

diff --git a/titan/features/syringe_services.py b/titan/features/syringe_services.py
@@ -6,7 +6,6 @@
 
 
 class SyringeServices(base_feature.BaseFeature):
-
     name = "syringe_services"
 
     enrolled_risk = 0.0

diff --git a/titan/features/vaccine.py b/titan/features/vaccine.py
@@ -9,7 +9,6 @@
 
 
 class Vaccine(base_feature.BaseFeature):
-
     name = "vaccine"
     stats = ["vaccine"]
     """

diff --git a/titan/interactions/base_interaction.py b/titan/interactions/base_interaction.py
@@ -3,7 +3,6 @@
 
 
 class BaseInteraction:
-
     name: str = ""
     """Name of interaction in the params file."""
 

diff --git a/titan/interactions/injection.py b/titan/interactions/injection.py
@@ -6,7 +6,6 @@
 
 
 class Injection(base_interaction.BaseInteraction):
-
     name = "injection"
 
     @classmethod

diff --git a/titan/interactions/pca.py b/titan/interactions/pca.py
@@ -5,7 +5,6 @@
 
 
 class PCA(base_interaction.BaseInteraction):
-
     name = "pca"
 
     @classmethod

diff --git a/titan/interactions/sex.py b/titan/interactions/sex.py
@@ -5,7 +5,6 @@
 
 
 class Sex(base_interaction.BaseInteraction):
-
     name = "sex"
 
     @classmethod

diff --git a/titan/location.py b/titan/location.py
@@ -129,7 +129,6 @@ def add_weight(d, v, w):
 # * how will mobility be implemented?
 # * assorting?
 class LocationEdge:
-
     next_edge_id = 0
 
     @classmethod

diff --git a/titan/output.py b/titan/output.py
@@ -301,7 +301,7 @@ def print_components(
             "\tdensity\tEffectiveSize\tdeg_cent\n"
         )
 
-    for (id, comp) in enumerate(components):
+    for id, comp in enumerate(components):
         num_nodes = comp.number_of_nodes()
 
         average_size = effective_size(comp) / num_nodes

diff --git a/titan/population.py b/titan/population.py
@@ -411,7 +411,6 @@ def update_partner_assignments(self, t: int):
             while eligible_agents:
                 agent = eligible_agents.popleft()
                 if len(agent.partners[bond]) < agent.target_partners[bond]:
-
                     # no match
                     if self.update_agent_partners(agent, bond, network_components):
                         attempts[agent] += 1

diff --git a/titan/utils.py b/titan/utils.py
@@ -391,7 +391,7 @@ def grid_file_to_edges(file_path: str, diagonal_neighbors: bool = False) -> Dict
                     add_edge(edges, loc, grid[i + 1][j - 1])
 
     res = {}
-    for (i, edge) in enumerate(edges):
+    for i, edge in enumerate(edges):
         res[f"edge_{i+1}"] = {"location_1": edge[0], "location_2": edge[1]}
 
     return res
Original file line number	Diff line number	Diff line change
Expand Up		@@ -6,7 +6,6 @@


		class BaseExposure:

		name: str = ""
		"""Name of exposure in the params file. Also used to name the attribute in Agent"""

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-Original file line number
+Diff line change
@@ Expand Up / @@ -8,7 +8,6 @@ @@
     class HIV(base_exposure.BaseExposure):
         name: str = "hiv"
         stats: List[str] = ["hiv", "hiv_dx", "hiv_aids", "hiv_new", "hiv_dx_new"]
         """
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,7 +5,6 @@


		class ExternalExposure(base_feature.BaseFeature):

		name = "external_exposure"

		def __init__(self, agent: "agent.Agent"):
Expand Down
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Expand Up		@@ -4,7 +4,6 @@


		class PartnerTracing(base_feature.BaseFeature):

		name = "partner_tracing"

		def __init__(self, agent: "agent.Agent"):
Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -6,7 +6,6 @@


		class SyringeServices(base_feature.BaseFeature):

		name = "syringe_services"

		enrolled_risk = 0.0
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Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,7 +3,6 @@


		class BaseInteraction:

		name: str = ""
		"""Name of interaction in the params file."""

Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -6,7 +6,6 @@


		class Injection(base_interaction.BaseInteraction):

		name = "injection"

		@classmethod
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Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,7 +5,6 @@


		class PCA(base_interaction.BaseInteraction):

		name = "pca"

		@classmethod
Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -5,7 +5,6 @@


		class Sex(base_interaction.BaseInteraction):

		name = "sex"

		@classmethod
Expand Down