Merge pull request #29 from openmethane/fix-paths

Fix paths

.github/workflows/ci.yaml

@@ -24,7 +24,7 @@ jobs:
           venv-id: "tests-${{ runner.os }}"
       - name: Run tests
         run: |
-         poetry run pytest -r a -v tests
+         make test
         env:
           CDSAPI_KEY: ${{ secrets.CDSAPI_ADS_KEY }}
           CDSAPI_URL: https://ads.atmosphere.copernicus.eu/api/v2

.gitignore

@@ -1,20 +1,261 @@
-__pycache__
+# Created by https://www.toptal.com/developers/gitignore/api/python
+# Edit at https://www.toptal.com/developers/gitignore?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio, WebStorm and Rider
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# AWS User-specific
+.idea/**/aws.xml
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/artifacts
+# .idea/compiler.xml
+# .idea/jarRepositories.xml
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# SonarLint plugin
+.idea/sonarlint/
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
+
+# VS Code
+.vscode/launch.json
+.vscode/settings.json
+
+# Custom ignores
+
 outputs
 inputs
 intermediates
-experiments
-dist
-src/openmethane_prior.egg-info/
-.env
-.idea
 
 !outputs/README.md
 !inputs/README.md
 !intermediates/README.md
-.vscode/launch.json
-.vscode/settings.json
-domain.ipynb
-
-# Virtual environment
-venv
-.venv

Makefile

@@ -34,3 +34,7 @@ ruff-fixes:  # Run ruff on the project
 	poetry run ruff format .
 	poetry run ruff check --fix .
 	poetry run ruff format .
+
+.PHONY: test
+test:  ## Run the tests
+	poetry run python -m pytest -r a -v tests

pyproject.toml

@@ -91,4 +91,4 @@ ignore = [
 convention = "numpy"
 
 [tool.ruff.lint.isort]
-known-first-party = ["src"]
+known-first-party = ["src", "scripts"]

src/openmethane_prior/layers/omFugitiveEmis.py

@@ -24,15 +24,14 @@
 
 import numpy as np
 import pandas as pd
+
 from openmethane_prior.omInputs import (
     coalPath,
     domainProj,
     oilGasPath,
     sectoralEmissionsPath,
 )
-from openmethane_prior.omInputs import (
-    domainXr as ds,
-)
+from openmethane_prior.omInputs import domainXr as ds
 from openmethane_prior.omOutputs import convert_to_timescale, sumLayers, write_layer
 
 

tests/test_domain_json.py

@@ -1,18 +1,13 @@
 # work around until folder structure is updated
-import os
-import sys
-
-# insert root directory into python module search path
-sys.path.insert(1, os.getcwd())
-
 import json
+import os
 from io import StringIO
 from pathlib import Path
 
 import pytest
-from scripts.omDomainJSON import write_domain_json
 
 from openmethane_prior.omInputs import domainPath
+from scripts.omDomainJSON import write_domain_json
 
 ROOT_DIRECTORY = Path(__file__).parent.parent
 

tests/test_om_prior.py

@@ -1,8 +1,6 @@
 import datetime
 import os
 import subprocess
-import sys
-from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -13,10 +11,7 @@
 from openmethane_prior.layers.omGFASEmis import downloadGFAS
 from openmethane_prior.omInputs import livestockDataPath, sectoralEmissionsPath
 from openmethane_prior.omUtils import getenv, secsPerYear
-
-root_path = Path(__file__).parent.parent
-sys.path.insert(1, os.path.join(root_path, "scripts"))
-from omDownloadInputs import download_input_files, downloads, remote  # noqa: E402
+from scripts.omDownloadInputs import download_input_files, downloads, remote
 
 
 @pytest.fixture(scope="session")