Merge pull request #119 from GNS-Science/move-resources-and-scripts

Move resources and scripts under top level package

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.13.4
+current_version = 0.13.5
 commit = True
 tag = True
 

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## [0.13.5] 2024-17-12
+
+### Changed
+- moved scripts and resources packages to be under nzshm_model package
+
 ## [0.13.4] 2024-12-12
 
 ### Added

docs/scripts.md

@@ -1,11 +1,11 @@
 # CLI Reference
 
 ::: mkdocs-click
-    :module: scripts.cli
+    :module: nzshm_model.scripts.cli
     :command: cli
     :prog_name: cli
 
 ::: mkdocs-click
-    :module: scripts.slt
+    :module: nzshm_model.scripts.slt
     :command: slt
     :prog_name: slt

docs/scripts/cli.md

@@ -1,5 +1,5 @@
 ::: mkdocs-click
-    :module: scripts.cli
+    :module: nzshm_model.scripts.cli
     :command: cli
     :prog_name: cli
 

docs/scripts/slt.md

@@ -1,4 +1,4 @@
 ::: mkdocs-click
-    :module: scripts.slt
+    :module: nzshm_model.scripts.slt
     :command: slt
     :prog_name: slt

mkdocs.yml

@@ -6,7 +6,6 @@ repo_name: GNS-Science/nzshm-model
 watch:
   - nzshm_model
   - docs
-  - scripts
 nav:
   - Home: index.md
   - Installation: installation.md

nzshm_model/__init__.py

@@ -43,4 +43,4 @@
 from .model_version import CURRENT_VERSION, all_model_versions, get_model_version, versions
 
 # Python package version is different than the NSHM MODEL version !!
-__version__ = '0.13.4'
+__version__ = '0.13.5'

nzshm_model/branch_registry.py

@@ -16,15 +16,14 @@
 
 import csv
 import hashlib
-
-# import io
-import pathlib
+import importlib.resources as resources
 from dataclasses import asdict, dataclass
 from typing import IO, Any, Optional
 
 HEADERS = ['hash_digest', 'identity', 'extra']
-GMM_REGISTRY_CSV = pathlib.Path(__file__).parent.parent / 'resources' / 'gmm_branches.csv'
-SOURCE_REGISTRY_CSV = pathlib.Path(__file__).parent.parent / 'resources' / 'source_branches.csv'
+RESOURCES_DIR = resources.files('nzshm_model.resources')
+GMM_REGISTRY_CSV = RESOURCES_DIR / 'gmm_branches.csv'
+SOURCE_REGISTRY_CSV = RESOURCES_DIR / 'source_branches.csv'
 
 
 def identity_digest(identity: str) -> str:
@@ -53,13 +52,13 @@ class Registry:
     @property
     def gmm_registry(self) -> 'BranchRegistry':
         if not self._gmms:
-            self._gmms = BranchRegistry().load(open(GMM_REGISTRY_CSV, 'r'))
+            self._gmms = BranchRegistry().load(GMM_REGISTRY_CSV.open('r'))
         return self._gmms
 
     @property
     def source_registry(self) -> 'BranchRegistry':
         if not self._sources:
-            self._sources = BranchRegistry().load(open(SOURCE_REGISTRY_CSV, 'r'))
+            self._sources = BranchRegistry().load(SOURCE_REGISTRY_CSV.open('r'))
         return self._sources
 
 

nzshm_model/model.py

@@ -14,7 +14,7 @@
 
 from .psha_adapter.hazard_config import HazardConfig, HazardConfigType
 
-RESOURCES_PATH = resources.files('resources')
+RESOURCES_PATH = resources.files('nzshm_model.resources')
 
 SLT_SOURCE_PATH = RESOURCES_PATH / "SRM_JSON"
 GMM_JSON_SOURCE_PATH = RESOURCES_PATH / "GMM_JSON"

pyproject.toml

@@ -1,20 +1,18 @@
 [tool.poetry]
 name = "nzshm-model"
-version = "0.13.4"
+version = "0.13.5"
 description = "The logic tree definitions, final configurations, and versioning of the New Zealand | Aotearoa National Seismic Hazard Model"
 authors = ["Chris DiCaprio <[email protected]>", "Chris Chamberlain <[email protected]>"]
 license = "AGPL3"
 readme = "README.md"
 packages = [
 	{include = "nzshm_model"},
-	{include = "resources"},
-	{include = "scripts"},
     {include = "tests", format = "sdist" }
 ]
 
 [tool.poetry.scripts]
-slt = 'scripts.slt:slt'
-model = 'scripts.cli:cli'
+slt = 'nzshm_model.scripts.slt:slt'
+model = 'nzshm_model.scripts.cli:cli'
 
 [tool.poetry.dependencies]
 python = ">=3.9,<4.0"
@@ -48,12 +46,12 @@ mkdocstrings = {extras = ["python"], version = "^0.27.0"}
 black  = { version = "^22.3"}
 bump2version = "^1.0.1"
 isort  = { version = "^5.8.0"}
-pytest = { version = "^6.2.4"}
-pytest-cov  = { version = "^2.12.0"}
 tox = "^4.2.8"
 mypy = "^1.8.0"
 flake8 = "^7.1.1"
 flake8-docstrings = {version = "^1.7.0", optional = true}
+pytest = "^8.3.4"
+pytest-cov = "^6.0.0"
 
 [tool.black]
 line-length = 120

setup.cfg

@@ -54,13 +54,12 @@ python =
 allowlist_externals = pytest
 extras =
 	test
-	scripts
 passenv = *
 setenv =
 	PYTHONPATH = {toxinidir}
 	PYTHONWARNINGS = ignore
 commands =
-	pytest --cov=nzshm_model --cov=scripts --cov-branch --cov-report=xml --cov-report=term-missing tests
+	pytest --cov=nzshm_model --cov-branch --cov-report=xml --cov-report=term-missing tests
 
 [testenv:format]
 allowlist_externals =
@@ -69,8 +68,8 @@ allowlist_externals =
 extras =
 	test
 commands =
-	isort nzshm_model scripts tests 
-	black nzshm_model scripts tests
+	isort nzshm_model tests
+	black nzshm_model tests
 
 [testenv:lint]
 allowlist_externals =
@@ -80,7 +79,7 @@ extras =
 	test
 commands =
 	flake8
-	mypy nzshm_model scripts tests resources
+	mypy nzshm_model tests
 
 [testenv:build]
 allowlist_externals =

tests/test_correlations_new.py

@@ -1,5 +1,5 @@
+import importlib.resources as resources
 import json
-from pathlib import Path
 
 from nzshm_model.logic_tree import SourceLogicTree
 from nzshm_model.logic_tree.source_logic_tree import SourceLogicTreeV1
@@ -8,7 +8,7 @@
 
 def test_v2_correlations():
 
-    slt_filepath = Path(__file__).parent.parent / "resources" / "SRM_JSON" / "nshm_v1.0.4.json"
+    slt_filepath = resources.files('nzshm_model.resources') / "SRM_JSON" / "nshm_v1.0.4.json"
     with slt_filepath.open() as slt_file:
         slt_v1 = SourceLogicTreeV1.from_dict(json.load(slt_file))
     slt_v2 = SourceLogicTree.from_source_logic_tree(slt_v1)

tests/test_logic_tree.py

@@ -1,6 +1,7 @@
 #! python test_logic_tree.py
 
 import dataclasses
+import importlib.resources as resources
 import itertools
 from pathlib import Path
 
@@ -120,7 +121,7 @@ def test_serialise_slt():
 
 class TestSourceLogicTreeSpecification:
     def test_slt_v8(self):
-        config = Path(__file__).parent.parent / 'resources' / 'SRM_LTs' / 'python' / 'SLT_v8_gmm_v2_final.py'
+        config = resources.files('nzshm_model.resources') / 'SRM_LTs' / 'python' / 'SLT_v8_gmm_v2_final.py'
         slt = from_config(config)
 
         slt_spec = slt.derive_spec()
@@ -154,7 +155,7 @@ def test_large_SLT_example_A_crustal(self):
 
 
 class TestFlattenedSourceLogicTree:
-    def setup(self):
+    def setup_method(self):
         ba0 = BranchAttributeSpec(name='C', long_name='area-magnitude scaling', value_options=[4.0, 4.1, 4.2])
         ba1 = BranchAttributeSpec(name='C', long_name='area-magnitude scaling', value_options=[4.1, 4.2, 4.3])
 

tests/test_slt_config.py

@@ -1,5 +1,6 @@
 #! test_module_import
 import dataclasses
+import importlib.resources as resources
 import json
 from pathlib import Path
 
@@ -87,7 +88,7 @@ def test_assemble_puy(self):
 class TestConfigSerialisation:
     @pytest.mark.parametrize("python_module", ['SLT_v9p0p0.py', 'SLT_v8_gmm_v2_final.py'])
     def test_slt_dict_to_json(self, python_module):
-        config = Path(__file__).parent.parent / 'resources' / 'SRM_LTs' / 'python' / python_module
+        config = resources.files('nzshm_model.resources') / 'SRM_LTs' / 'python' / python_module
         slt = from_config(config)
         obj = dataclasses.asdict(slt)
         jsonish = json.dumps(obj, indent=2)
@@ -97,7 +98,7 @@ def test_slt_dict_to_json(self, python_module):
     @pytest.mark.parametrize("python_module", ['SLT_v9p0p0.py', 'SLT_v8_gmm_v2_final.py'])
     def test_slt_v8_round_trip(self, python_module):
 
-        config = Path(__file__).parent.parent / 'resources' / 'SRM_LTs' / 'python' / python_module
+        config = resources.files('nzshm_model.resources') / 'SRM_LTs' / 'python' / python_module
         slt = from_config(config)
         obj = dataclasses.asdict(slt)
         jsonish = json.dumps(obj, indent=2)
@@ -119,7 +120,7 @@ def test_slt_v8_round_trip(self, python_module):
 
 class TestFromConfig:
     def test_slt_v8(self):
-        config = Path(__file__).parent.parent / 'resources' / 'SRM_LTs' / 'python' / 'SLT_v8_gmm_v2_final.py'
+        config = resources.files('nzshm_model.resources') / 'SRM_LTs' / 'python' / 'SLT_v8_gmm_v2_final.py'
         slt = from_config(config)
         print(slt)
         assert slt.fault_system_lts[0].branches[-1].values[0].name == 'dm'