Tags: DESI-UR/VAST
Tags
Internals rewrite (#94) * Add mask input option, galaxy ID tracking * Fix bug allowing zero-volume cells in zones * Add third ZOBOV pruning method * Fix inclusion of isolated zones * Update Vsquared documentation * Fix triangle void IDs * Remove old Vsquared directory * Update V2 unit tests * Fix typo * Remove merge conflict message * Finished majority of rewrite * Fix length of voronoi volume array for periodic boundary conditions. * Completed internals rewrite, achieving average speedup of 1.5x versus old method * Some big cleanup of old commented out code and such * cleanup * updating version number * Updating tests.yml to use pytest and not pytest-runner as pytest-runner appears to be deprecated * Updating tests.yml to use pytest and not pytest-runner as pytest-runner appears to be deprecated * Updating tests.yml to use pytest and not pytest-runner as pytest-runner appears to be deprecated * Updating tests.yml to use pytest and not pytest-runner as pytest-runner appears to be deprecated * Updating tests.yml to use pytest and not pytest-runner as pytest-runner appears to be deprecated * Internals updates; Added grid_origin parameter to find_voids; hopefully fixed Vsquared unit tests * possibly fixed v2 unit tests * Updated all version numbers * Updated example scripts Co-authored-by: Dylan Veyrat <[email protected]>
Vf boundary (#91) * Updated directory structure for consistency * Fixed file paths to reflect current repo structure, and cleaned up erroneous comments * Added missing comma to sample V2 script, code formatting adjustments * Fixed fake void galaxy removal * Added 'edge' column to truth table, other minor changes * Added min_maximal_radius to generate_mask so that it is not hard-coded * Added pts_per_unit_volume kwarg to find_voids * Fixed indexing issue for identifying edge voids * Changed deprecated np.bool to np.bool_ * Added field galaxies to find_voids so that the hole grid is defined based on both wall and field galaxies * Cleaning up doc strings, increasing version number to reflect change in find_voids function call * Commented out early return for next galaxy locator * Added field galaxies back into find_voids * Creating debug file, doc string cleanup * Switched _query_first variables from ijk to pqr label * Doc string cleanup and adding VF unit tests * Moving changes to Ubuntu * Added changelog file for tracking version information * Added unit vector direction for co-linear case, tested new 4th galaxy procedure against unit tests and SDSS DR7 successfully * Updated version to 1.2.2 * updated changelog * Update VoidFinder void truth files for unit tests * Trying to debug VF unit test for Python 3.9 * If output does not match truth, print both tables * Changed void comparisons to use np.allclose instead of equality * Readded maximal and hole files to pytest cleanup * Adding print statements when find_void test fails * Commenting out print statements, because apparently it passes now (?) * Adding the print statements in for the holes comparison, as apparently that one is now failing (?) * Changed print statement for readability * Increased galaxy density and sorted hole tables * Commenting out print lines Co-authored-by: Kelly <[email protected]>
Switch to pkgutil-style namespace package structure. (#25) * Add pkgutil-style namespace package. * Add pkgutil-style namespace package. * Add setup script and version info. * Add voidfinder interface. * Add cython build scripts. * Add legacy submodule. * Add viz folder. Check on build steps. * Add volume submodule. * Add unit test folder. * Add Cython type definitions. * Cythonize and import voidfinder functions. * Remove conflicting & unmaintained tests. * Update import in unit test. * Set up separate V^2 sub-package. * Enable V^2 as a standalone sub-package. * Remove old python subfolder. * Remove empty folder. * Fix version include. * Enable version access. * Remove old python code directory. * Fix versioning command. * Update version command. * Update version to 0.2.0. * Revert version. Add util docstrings. * Add docstrings, test interface. * Fix docstring omission. * Move old python/scripts dir here. * Clean up imports for new structure. * Fix V^2 import statements * Update V^2 README * Update setup.py to use string version ID. * Remove git version management code. * Harmonize with master/Kelly-branch. * Temporarily restore python folder. * Harmonize scripts with master/Kelly-branch. * Harmonize with master/Kelly-branch. * Harmonize with master/Kelly-branch. * Harmonize with master/Kelly-branch. * Delete python directory. * Move cython stuff below requires line. * Remove git versioning from setup.py. * Update version info and docstrings. * Set version in submodule __init__.py. * Move __version__ to package __init__.py. * Get version from sub-package __init__.py. * Update version numbers. * Update READMEs to reflect new package structure. * Add CircleCI YAML configuration. * Remove duplicate circleci directory. * Put requirements into an external file. * Add external list of requirements. * Add test packages to requirements. * Update circleci config. * Config broken. * Try a refactor of config.yml. * CircleCI doesn't like me. * Simplify. * Even simpler. * Syntax issue. * Try working_directory keyword. * syntax fix * Remove working_directory. * Try a named job. * Try renaming job. * Revert changes. * Change job name. * Add working (?) CircleCI hooks for VoidFinder. * Add astropy+matplotlib to requirements. * Add astropy to listed requirements. * Update cache location. * Undo caching of environment. * Try one more cache location. * Comment out workflows for a second. * Try out workflows. * Try VF+V2 workflow with caching. * Manually update cache. * Remove cruft and add useful comments. * Add V^2 unit tests * Major code and repo clean-up * Re-adding volume-limited DR7 data for example Co-authored-by: Segev BenZvi <[email protected]> Co-authored-by: Dylan Veyrat <[email protected]> Co-authored-by: Kelly <[email protected]>