Update and freeze deps #186
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Dec 11, 2024
* Create pythonpublish.yml * updated to 0.1.0 including pip support * Create .pypirc * removed token * corrected file name * removed GDAL dep * updated file content * corrected folder name * version 0.1.1, now REALLY with pip and github actions * updated pypi installation instruction * added quantiles * added sanity checks * writing geojson instead shp * Bump pip from 20.0.2 to 21.1 Bumps [pip](https://github.com/pypa/pip) from 20.0.2 to 21.1. - [Release notes](https://github.com/pypa/pip/releases) - [Changelog](https://github.com/pypa/pip/blob/main/NEWS.rst) - [Commits](pypa/pip@20.0.2...21.1) --- updated-dependencies: - dependency-name: pip dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump ipython from 7.13.0 to 7.16.3 in /docs Bumps [ipython](https://github.com/ipython/ipython) from 7.13.0 to 7.16.3. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@7.13.0...7.16.3) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump ipython from 7.13.0 to 7.16.3 Bumps [ipython](https://github.com/ipython/ipython) from 7.13.0 to 7.16.3. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@7.13.0...7.16.3) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump numpy from 1.18.1 to 1.21.0 Bumps [numpy](https://github.com/numpy/numpy) from 1.18.1 to 1.21.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt) - [Commits](numpy/numpy@v1.18.1...v1.21.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump numpy from 1.18.1 to 1.21.0 in /docs Bumps [numpy](https://github.com/numpy/numpy) from 1.18.1 to 1.21.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst.txt) - [Commits](numpy/numpy@v1.18.1...v1.21.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump numpy from 1.21.0 to 1.22.0 in /docs (#150) Bumps [numpy](https://github.com/numpy/numpy) from 1.21.0 to 1.22.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst) - [Commits](numpy/numpy@v1.21.0...v1.22.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump numpy from 1.21.0 to 1.22.0 (#151) Bumps [numpy](https://github.com/numpy/numpy) from 1.21.0 to 1.22.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/HOWTO_RELEASE.rst) - [Commits](numpy/numpy@v1.21.0...v1.22.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump nbconvert from 5.6.1 to 6.3.0 (#153) Bumps [nbconvert](https://github.com/jupyter/nbconvert) from 5.6.1 to 6.3.0. - [Release notes](https://github.com/jupyter/nbconvert/releases) - [Commits](jupyter/nbconvert@5.6.1...6.3.0) --- updated-dependencies: - dependency-name: nbconvert dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump nbconvert from 5.6.1 to 6.3.0 in /docs (#152) Bumps [nbconvert](https://github.com/jupyter/nbconvert) from 5.6.1 to 6.3.0. - [Release notes](https://github.com/jupyter/nbconvert/releases) - [Commits](jupyter/nbconvert@5.6.1...6.3.0) --- updated-dependencies: - dependency-name: nbconvert dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump setuptools from 49.6 to 65.5.1 in /docs (#158) Bumps [setuptools](https://github.com/pypa/setuptools) from 49.6 to 65.5.1. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/CHANGES.rst) - [Commits](pypa/setuptools@v49.6.0...v65.5.1) --- updated-dependencies: - dependency-name: setuptools dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump nbconvert from 6.3.0 to 6.5.1 (#154) Bumps [nbconvert](https://github.com/jupyter/nbconvert) from 6.3.0 to 6.5.1. - [Release notes](https://github.com/jupyter/nbconvert/releases) - [Commits](jupyter/nbconvert@6.3.0...6.5.1) --- updated-dependencies: - dependency-name: nbconvert dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump nbconvert from 6.3.0 to 6.5.1 in /docs (#155) Bumps [nbconvert](https://github.com/jupyter/nbconvert) from 6.3.0 to 6.5.1. - [Release notes](https://github.com/jupyter/nbconvert/releases) - [Commits](jupyter/nbconvert@6.3.0...6.5.1) --- updated-dependencies: - dependency-name: nbconvert dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump wheel from 0.33.6 to 0.38.1 in /docs (#156) Bumps [wheel](https://github.com/pypa/wheel) from 0.33.6 to 0.38.1. - [Release notes](https://github.com/pypa/wheel/releases) - [Changelog](https://github.com/pypa/wheel/blob/main/docs/news.rst) - [Commits](pypa/wheel@0.33.6...0.38.1) --- updated-dependencies: - dependency-name: wheel dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump setuptools from 49.6 to 65.5.1 (#157) Bumps [setuptools](https://github.com/pypa/setuptools) from 49.6 to 65.5.1. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/CHANGES.rst) - [Commits](pypa/setuptools@v49.6.0...v65.5.1) --- updated-dependencies: - dependency-name: setuptools dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump ipython from 7.16.3 to 8.10.0 in /docs (#159) Bumps [ipython](https://github.com/ipython/ipython) from 7.16.3 to 8.10.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@7.16.3...8.10.0) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump ipython from 7.16.3 to 8.10.0 (#160) Bumps [ipython](https://github.com/ipython/ipython) from 7.16.3 to 8.10.0. - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@7.16.3...8.10.0) --- updated-dependencies: - dependency-name: ipython dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * updated dependencies (#161) * v0.1.2 (#162) * updated dependencies * correct dtype of list with selection conflict type * got rid of fiona requirement * improved downloading of example data * deprecated plotting for now as sklearn API has changed * v0.1.2 * Bump pip from 21.1 to 23.3 (#183) Bumps [pip](https://github.com/pypa/pip) from 21.1 to 23.3. - [Changelog](https://github.com/pypa/pip/blob/main/NEWS.rst) - [Commits](pypa/pip@21.1...23.3) --- updated-dependencies: - dependency-name: pip dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump jinja2 from 2.11.3 to 3.1.3 in /docs (#184) Bumps [jinja2](https://github.com/pallets/jinja) from 2.11.3 to 3.1.3. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](pallets/jinja@2.11.3...3.1.3) --- updated-dependencies: - dependency-name: jinja2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Update and freeze deps (#186) * some cleaning up * precommit hooks * models.py as object-based * object based machine_learning.py * moving functions here * object based models.py * removed some unnecesssary functions * updates because of moved function * starting to clean up data.py mess * Object based and more (#187) * cleaning up evaluation.py * parsing and collecting of settings/configurations in separate file * separate file for I/O functions * clean up * removed outdated tests * improving selection.py * Update CODE_OF_CONDUCT.md * updated and moved functions in conflicts.py * cosmetic changes to machine_learning.py * put all neighbours related functions in one file * updating data.py, resp. what is now called xydata.py * moved run_prediction func from ppeline.py to models.py * updated cli script * Debug copro runner (#188) * works up to ML part * debugging some eval functions * reference run works via command line; removed feature importance for now * loop over n_runs now part of models.py * rename * minor improvements * defining projection period works now (again) * projections succesfully run * completed docstrings and typehints * improving console out * watprovID now always a kwarg (#189) * Fix rtd (#190) * restart doc * updated dependencis * removed out-dated duplicate * next take * added pydata-sphinx-theme dep * using conda for rtd * bla * add mock * sphinx works locally at least * splitting docs in source and make * blabla * no copro dep in conf.py * add installation instructions * added static data * Fix rtd (#191) * restart doc * updated dependencis * removed out-dated duplicate * next take * added pydata-sphinx-theme dep * using conda for rtd * bla * add mock * sphinx works locally at least * splitting docs in source and make * blabla * no copro dep in conf.py * add installation instructions * added static data * added API partially * updated installation * GridsearchCV (#192) * possible to tune hyperparameters of each RFC instance * n_jobs and verbose as click options * applying gridsearchcv works as expected * updated example settings * extended documentation * computing permutation importance for each run n with 10 permutations (#193) * lag time as constant; removed distutils * Bump setuptools from 69.0.3 to 70.0.0 (#198) Bumps [setuptools](https://github.com/pypa/setuptools) from 69.0.3 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v69.0.3...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump scikit-learn from 1.3.2 to 1.5.0 (#197) Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 1.3.2 to 1.5.0. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@1.3.2...1.5.0) --- updated-dependencies: - dependency-name: scikit-learn dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add ACLED support and use "yaml" file type for model settings (#199) * first steps * Switch from cfg to yaml (#194) * parse YAML file * parsing settings from YAML-file works * improved conflict property selection based on YAML-file input * fix _clip_to_extent * reading indicator data works, also with options * adding poly_id and conflict_id * added todos * fixed problem with perm. importance and debugged workflow to be compatible with yaml input * add KFold to GridSearchCV * Better NaN handling and dataframe support (#200) * option for either Regression or Classification model * fine tuned selection of conflict data points * option to provide ML target variable * use simulation_name as output dir * data extraction from netCDF files in a separate function * target variable and estimator used determined in main script * should belong to previous commit * first step towards flexible target_vars when extracting conflict (Y) data * added class docstrings * constructing X and Y data as dataframes instead of arrays * no log-scale support for now, more consistent treatment of polygons w/o feature data * removing all polygons with 1 or more NaNs * fully pd.dataframe support implemented * save only selected conflicts which fall in simulation period * finetuning print output * Fix/projections (#201) * option for either Regression or Classification model * fine tuned selection of conflict data points * option to provide ML target variable * use simulation_name as output dir * data extraction from netCDF files in a separate function * target variable and estimator used determined in main script * should belong to previous commit * first step towards flexible target_vars when extracting conflict (Y) data * added class docstrings * constructing X and Y data as dataframes instead of arrays * no log-scale support for now, more consistent treatment of polygons w/o feature data * removing all polygons with 1 or more NaNs * fully pd.dataframe support implemented * save only selected conflicts which fall in simulation period * finetuning print output * no random state set for Kfold in GridSearchCV to ensure all n models are fitted on different data * better handling of cores via command line * remove content of output dir to avoid conflicts with expected files * settings parsed for projections with new yaml file structure * udpated docstring for load_estimators * fixed definition of projection period * reinitated initiate_X_data function * saving files as GPKG instead GeoJSON * no output for None output from rasterstats * make run_prediction() work * apply isort * no ML target var for nwo * fix Geopandas driver * corrected number of function arguments * Bump scikit-learn from 0.22.1 to 1.5.0 in /docs (#205) Bumps [scikit-learn](https://github.com/scikit-learn/scikit-learn) from 0.22.1 to 1.5.0. - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@0.22.1...1.5.0) --- updated-dependencies: - dependency-name: scikit-learn dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump setuptools from 65.5.1 to 70.0.0 in /docs (#204) Bumps [setuptools](https://github.com/pypa/setuptools) from 65.5.1 to 70.0.0. - [Release notes](https://github.com/pypa/setuptools/releases) - [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst) - [Commits](pypa/setuptools@v65.5.1...v70.0.0) --- updated-dependencies: - dependency-name: setuptools dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump jinja2 from 3.1.3 to 3.1.4 in /docs (#203) Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](pallets/jinja@3.1.3...3.1.4) --- updated-dependencies: - dependency-name: jinja2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
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Updated conda environment, with frozen dependency versions.
Also, started to convert code to object based and removed some unnecessary stuff.