ciceroscm 0.0.0__tar.gz

ciceroscm-0.0.0/.bandit.yml

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+exclude_dirs:
+  - ciceroscm/_version.py

ciceroscm-0.0.0/.coveragerc

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+[run]
+branch = True
+source = ciceroscm
+omit = *_version.py,*testing.py
+
+[report]
+fail_under = 90
+exclude_lines =
+    if self.debug:
+    pragma: no cover
+    raise NotImplementedError
+    if __name__ == .__main__.:
+ignore_errors = True

ciceroscm-0.0.0/.gitattributes

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+src/cicero-scm/_version.py export-subst

ciceroscm-0.0.0/.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug Report
+about: Write a report to help us improve
+
+---
+
+**Describe the bug**
+
+A clear and concise description of what the bug is, in particular:
+
+- What did you do?
+- What actually happened?
+- What did you expect to happen?
+
+**Failing Test**
+
+Please put code (ideally in the form of a unit test) which fails below
+
+**Screenshots**
+
+If applicable, add screenshots to help explain your problem.
+
+**System (please complete the following information):**
+
+ - OS: [e.g. Windows, Linux, macOS]
+ - Python and openscm commit/version [e.g. Python 3.5]
+
+**Additional context**
+
+Add any other context about the problem here.

ciceroscm-0.0.0/.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature Request
+about: Suggest an idea for this project
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+
+A clear and concise description of what the problem is. E.g. It's annoying that I always have to [...]
+
+**Describe the solution you'd like**
+
+A clear and concise description of the solution you would like to see.
+
+**Describe alternatives you've considered**
+
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+
+Add any other context or screenshots about the feature request here.

ciceroscm-0.0.0/.github/pull_request_template.md

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+<Please replace this paragraph by a description of what this PR does and alter the TODO-list below to what applies here. Please make a 'draft PR' to begin and then only mark it as ready for review once all the relevant points are done.>
+
+- [ ] Tests added
+- [ ] Documentation added
+- [ ] Example added (in the documentation, to an existing notebook, or in a new notebook)
+- [ ] Description in ``CHANGELOG.rst`` added (single line such as: ``(`#XX <https://github.com/ciceroOslo/ciceroscm/pull/XX>`_) Added feature which does something``)

ciceroscm-0.0.0/.github/workflows/ci-cd-workflow.yml

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+name: CiceroSCM-Runner CI-CD
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v*'
+  pull_request:
+
+jobs:
+  linting-and-docs:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.12']
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - name: Setup python
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dev dependencies
+      # why pandas 1.1.5 breaks pylint, I do not know
+      run: |
+        pip install --upgrade pip wheel
+        pip install -e .[dev]
+    - name: Formatting and linters
+      run: |
+        black --version
+        black --check src tests --exclude ciceroscm/_version.py
+        isort --version
+        isort --check-only --quiet --recursive src tests
+        pydocstyle --version
+        pydocstyle src
+        bandit --version
+        bandit -c .bandit.yml -r src
+        ruff version
+        ruff check src tests
+        pylint --version
+        pylint src
+    # Muting docs for now, will try to make transition to other package manager for this eventually
+    #- name: Build docs
+      # treat warnings as errors (-W)...
+      # ...but not when being nitpicky (-n)
+      #run: |
+          #sphinx-build -M html docs/source docs/build -qW
+          # Muted coverage-test for now
+          #sphinx-build -M html docs/source docs/build -Eqn -b coverage
+          #if [[ -s docs/build/html/python.txt ]]
+          #then
+          #    echo
+          #    echo \"Error: Documentation missing:\"
+          #    echo
+          #    cat docs/build/html/python.txt
+          #    exit 1
+          #fi
+
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+
+        python-version: ['3.12', '3.10', '3.11']
+    env:
+      MIN_COVERAGE: 90
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - name: Setup python
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install test dependencies
+      run: |
+        pip install --upgrade pip wheel
+        pip install -e .[tests,models]
+    - name: Test with pytest
+      run: |
+        pytest tests -r a --cov=ciceroscm --cov-report='' --cov-fail-under=$MIN_COVERAGE
+
+  test-notebooks:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.12', '3.10', '3.11']
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - name: Setup python
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install notebook dependencies
+      run: |
+        pip install --upgrade pip wheel
+        pip install -e .[tests,models,notebooks]
+    - name: Test notebooks with nbval
+      run: |
+          pytest notebooks -r a --nbval-lax --sanitize-with tests/notebook-tests.cfg --no-cov
+    - name: Test notebooks strictly
+      if: matrix.python-version == '3.12'
+      run: |
+          pytest notebooks -r a --nbval --nbval-sanitize-with tests/notebook-tests.cfg --no-cov
+
+
+  test-install:
+
+    needs: [build,linting-and-docs]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.12', '3.10', '3.11']
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - name: Setup python
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install
+      run: |
+        pip install --upgrade pip wheel
+        pip install .
+    - name: Test installation
+      run: |
+        pip list
+        python scripts/test_install.py
+
+  # Commenting this out for now till we figure out how to do distributions with
+  # newer type of package manager
+  #create-dist:
+
+    #needs: [build,linting-and-docs]
+
+  #  runs-on: ubuntu-latest
+  #  strategy:
+  #    matrix:
+  #      python-version: ['3.12']
+
+  #  steps:
+  #  - name: Checkout repository
+  #    uses: actions/checkout@v4
+  #  - name: Setup python
+  #    uses: actions/setup-python@v1
+  #    with:
+  #      python-version: 
+  #  - name: Install dependencies
+  #    run: |
+  #      pip install --upgrade pip wheel
+  #      pip install -e .[dev]
+  #  - name: Create package
+  #    run: |
+  #      python sdist bdist_wheel --universal
+  #      twine check dist/*
+  #  - uses: actions/upload-artifact@v4
+  #    with:
+  #      name: dist
+  #      path: dist
+
+
+  #deploy-pypi:
+
+  #  needs: [test-install,create-dist]
+  #  if: startsWith(github.ref, 'refs/tags/v')
+  #  runs-on: ubuntu-latest
+  #  strategy:
+  #    matrix:
+  #      python-version: ['3.12']
+
+  #  steps:
+  #  - uses: actions/download-artifact@v4
+  #    with:
+  #      name: dist
+  #      path: dist
+  #  - name: Publish package to PyPI
+  #    uses: pypa/gh-action-pypi-publish@release/v1
+  #    with:
+  #      user: __token__
+  # NBNB next line is missing two curly brackets at the end
+  #      password: ${{ secrets.pypi_api_token

ciceroscm-0.0.0/.github/workflows/publish.yml

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+name: Upload Python Package to PyPI when a Release is Created
+
+on: workflow_dispatch
+#  release:
+#    types: [created]
+
+jobs:
+  pypi-publish:
+    name: Publish release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/ciceroscm
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip wheel setuptools build twine
+          pip install -e .[dev]
+      - name: Build package
+        run: |
+          python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.13.0

ciceroscm-0.0.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Tempfiles
+*~
+*#
+*.png
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+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/
+
+# 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
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/
+
+# Vscode
+.vscode/

ciceroscm-0.0.0/.pylintrc

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+[MASTER]
+ignore=_version.py
+load-plugins=
+    pylint.extensions.bad_builtin,
+    pylint.extensions.check_elif,
+    pylint.extensions.docparams,
+    pylint.extensions.overlapping_exceptions,
+    pylint.extensions.redefined_variable_type
+
+# As a temporary workaround for https://github.com/PyCQA/pylint/issues/4577
+init-hook = "import astroid; astroid.context.InferenceContext.max_inferred = 500"
+
+[MESSAGES CONTROL]
+disable=
+    # handled by black
+    format,
+    import-error,
+    fixme
+
+[SIMILARITIES]
+min-similarity-lines=7
+ignore-comments=no
+ignore-docstrings=yes
+ignore-imports=yes
+
+[FORMAT]
+good-names=i,j,k,nt,yr,it,dt,rf,dT_glob,dT_NH,dT_SH,dT_glob_air,dT_glob_NH_air,dT_glob_SH_air,dT_glob_sea,q,dT_glob_NH_sea,dT_glob_SH_sea,dSL,dSL_ice,dSL_thermal,fs,fn,s,t,p0,p,t0,w,dz,tn,ts,z0,a,b,c,aa,bb,z,dn,ds,im,lm
+
+# Maximum number of characters on a single line. 
+max-line-length=90

ciceroscm-0.0.0/.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+    "python.testing.pytestArgs": [
+        "tests"
+    ],
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

ciceroscm-0.0.0/CHANGELOG.rst

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+Changelog
+=========
+
+All notable changes to this project will be documented in this file.
+
+The format is based on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`_, and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`_.
+
+The changes listed in this file are categorised as follows:
+
+    - Added: new features
+    - Changed: changes in existing functionality
+    - Deprecated: soon-to-be removed features
+    - Removed: now removed features
+    - Fixed: any bug fixes
+    - Security: in case of vulnerabilities.
+
+[Unreleased]
+---------------------------
+### Added
+- Deployment workflow to publish package to PyPI on manual trigger
+
+[Version 2.0.1]
+---------------------------
+### Added
+
+### Changed
+
+### Fixed
+
+- Ensure code can run when ozone is not changing, avoiding divide by zero.
+- Ensure calculation of airborne fraction gives nans when cumulative emissions are zero.
+- Fix bug affecting backward compatibility with not sending explicit carbon_cycle argument to concentrations_emissions_handler
+
+### Removed
+
+[Version 2.0.0]
+---------------------------
+
+### Changed
+- Simplified Tropospheric Ozone forcing calculation, using the same calculation throughout both before and after emstart 
+    (previous implementation relied on fossil fuel CO2 concentration likely for historical reasons of missing data).
+
+### Added
+
+- Option to chunk configuration distributions to allow for millions of member runs without killing memory
+- Option to output ozone and stratospheric water vapour effective radiative forcing in parallel run
+- _config_distro can now write distribution files with full setup metadata, and Distroconfig can read in files with or with out shared metadata.
+-  New structural switch functionality to allow for different structural configurations to be run for both carbon cycle and thermal model.
+- A simplified box carbon model and a simplified two-layer ocean model as structural options.
+- Option to run with regionally split aerosol species, also including functionality to make gaspamfile that supports this from forcing txt file.
+
+### Fixed
+
+- Skip precaclulation of empty concentrations matrix if emstart >= nyend
+- Carbon cycle output functioninng for concentrations runs
+- Parallel concentrations run pass back-calculated emissions series when prompted for Emissions|CO2
+- Fix so standalone concentrations_emissions_handler will run without explicitly sending carbon cycle model argument, ensuring backward compatibility.
+
+### Removed
+- Removed old calibrator code, as calibration is now done in a separate repository.
+- fnso (fraction of Northern hemisphere ocean to Southern hemisphere ocean) parameter removed from upwelling diffusion model. This parameter should be derived from the ratio between foan and foas, and not be something that can be set separately.
+
+[Version 1.5.0]
+---------------------------
+
+### Changed
+
+- Change so that non-changing gases are precalculated before a run in concentrations_emissions_handler.py to speed up and avoid looping over every component and looking up in pandas every timestep
+- Removed use of scmdata, and changed parallel output to be pandas to offload extra dependencies
+- Moved carbon cycle functionality out of concentrations_emissions_handler.py to separate module carbon_cycle_mod.py
+- Changed methodology for parametrised decay functions for biotic decay (rb_function) and mixed layer pulse response rs_function, imposing a few more consistency criteria on them and makeing them changable by a dictionary for each with keys "coeffs" and "timescales" with values that should be lists or np.arrays of coefficient and timescale values 
+- Upgrade infrasturucture for development
+- Output data / output files no longer include empty columns for species that don't make sense (landuse albedo emissions, concentrations for aerosols like BC etc)
+- Aerosol forcing is no longer scaled to a reference year, but is per change in annual emissions, this also changes aerosol forcing parameter values and units
+- Added NMVOC, NH3 and NOx as forcing aerosols
+- Changed default gaspam unit for SO2 to Tg_SO2 rather than Tg_S
+- Carbon cycle parameters now passed in a separate dictionary
+- Simplifying _config_distro
+
+
+### Added
+
+- Functionality to feedback current temperature change to the carbon cycle and have simple temperature feedback 
+- Functionality to back calculate CO2 emissions from concentrations
+- Functionality to calculate carbon fluxes to ocean and land
+- Functionality to calculate airborne fraction
+- Functionality to output new carbon cycle information
+- Functionality to output new carbon cycle information in parallel runs
+- Changeable parameter for the depth of the mixed_layer ocean seen by the carbon cycle
+- Newer gaspam files
+- Light check for emissions and gaspam file compatibility
+- Changeable ocean efficacy parameter to the upwelling diffusion model
+- Carbon cycle temperature feedbacks for mixed_layer ocean depth (sigmoid decline), 
+- Land primary production (optimum increase and threshold dampening decline) and
+- Ocean solubility (exponential scaling to limit)
+
+
+### Fixed
+
+- Removed `jupyter nbextension` from `Makefile` causing install errors
+- Locked numpy in requirements to below version 2 to work with scmdata for now
+- Fix error in flat N2O assumption in natural precalculate_natural_emissions.py script
+- Change logging messages for misisng parameters from warning to info
+- Fix bug in file cutting for read_inputfile in input_handler
+- Temporarily mute docs generation with sphinx on github as it is not working, plan to work in different method
+- Temporarily mute distribution generation, plan to work this back in with more updated package manager
+
+[Versions 1.1.1 and v1.1.0]
+---------------------------
+
+### Added
+
+- Support for flat natural emissions for NO2 and CH4 from gaspamfile as defaults
+- Update script to make natural emissions for NO2 and CH4 using ODE solution
+- Updates to default vulcanoe and solar forcing timeseries
+- Rationalising _band implementation using library for speed and readibility
+- Clearing out unused density realated methods
+- Made the fertilisation factor beta_f part a changeable parameter
+- Parallelisation wrapper for parallel runs
+- Config distributions support to make parameter distributions
+- Distrobution runner to run over distributions in parallel
+- Calibrator to make calibrated set of configurations based on calibration data
+- Made automatic plots more polished looking
+- Taking out unused parts from gaspam-file