csiborgtools/.gitignore

venv_csiborg/
share/
bin/
.bashrc
*.pyc
*/.ipynb_checkpoints/
plots/*
.vscode/settings.json
csiborgtools/fits/_halo_profile.py
csiborgtools/fits/_filenames.py
csiborgtools/fits/analyse_voids_25.py
scripts/*.out
build/*
.eggs/*
csiborgtools.egg-info/*
Pylians3/*
scripts/plot_correlation.ipynb
scripts/*.sh
venv/
.trunk/*
scripts_test/
scripts_plots/python.sh
scripts_plots/submit.sh
scripts_plots/*.out
scripts_plots/*.sh
notebooks/test.ipynb
scripts/mgtree.py
scripts/makemerger.py

*.out
*/python.sh
scripts_independent/clear.sh
Dump radial profile information (#48) * add radial position path * pep8 * Add basic fit profile dumping * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * Update TODO * Fix parts is None bug * Update nb 2023-04-26 23:18:30 +00:00			`venv_csiborg/`
first commit 2022-10-02 10:12:45 +00:00			`share/`
			`bin/`
			`.bashrc`
ignore *.pyc 2022-10-10 16:41:29 +00:00			`*.pyc`
ignore checkpoints 2022-10-11 12:47:26 +00:00			`*/.ipynb_checkpoints/`
Basic matching (#2) * add recarray manipulations * add cart to radec * add behav so x can be a list * add import * create empty files * ignore plots file * add planck data * add read_mmain file * add cols_to_structured import * use cols_to_structured * add cols_to_structued * add read_mmain import * add reading planck * add mass conversion * add brute force separation calculation * update nb * rename & int dtype * add func to get csiborg ids * add list to nd array conversion * add utils * rename file * add 2M++ * add read 2mpp * add 2mpp shortcut * add randoms generator * Change range of RA [0, 360] * fix ang wrapping * add code for sphere 2pcf * rm wrapping * optionally load only a few borgs * update nb 2022-10-18 18:41:20 +00:00			`plots/*`
ignore settings 2022-10-20 07:13:09 +00:00			`.vscode/settings.json`
Within halo work and NFW fit (#4) * add listing of snapshots * change distance to comoving * ignore cp files * rename nb * add str to list * add NFW profile shapes * add fits imports * Rename to Nsnap * in clumps_read only select props * make clumpid int * expand doc * add import * edit readme * distribute halos * add profile & posterior * add import * add import * add documentation * add rvs and init guess * update todo * update nb * add file * return end index too * change clump_ids format to int32 * skeleton of dump particle * update nb * add func to drop 0 clump indxs parts * add import * add halo dump * switch to float32 * Update TODO * update TODO * add func that loads a split * add halo object * Rename to clump * make post work with a clump * add optimiser * add Nsplits * ignore submission scripts * ignore .out * add dumppath * add job splitting * add split halos script * rename file * renaem files * rm file * rename imports * edit desc * add pick clump * add number of particles * update TODO * update todo * add script * add dumping * change dumpdir structure * change dumpdir * add import * Remove tqdm * Increase the number of splits * rm shuffle option * Change to remove split * add emojis * fix part counts in splits * change num of splits * rm with particle cut * keep splits * fit only if 10 part and more * add min distance * rm warning about not set vels * update TODO * calculate rho0 too * add results collection * add import * add func to combine splits * update TODO * add extract cols * update nb * update TODO 2022-10-30 20:16:56 +00:00			`csiborgtools/fits/_halo_profile.py`
			`csiborgtools/fits/_filenames.py`
			`csiborgtools/fits/analyse_voids_25.py`
			`scripts/*.out`
Particle match & file system & phase space (#11) * Create file system * add doc * add n_sim n_snap directly to paths * Move things to a single particle reader for consistency * add docstring * add srdcir, dumpdir and mmain_path * make boxunits work with paths * switch to using paths * add tempdumpdir * rm dependence on old functions * rm comment * rm unused import * go back to all imports * fix import bug * rm dependence on old functions * modernize code! * fix typo * fix typo * update fits to new data structureing * change docs * add julia repo * add setup * add install commands * ignore install files * add array flattening * update dependene * add positions reader * update manifest and projects * add func * update gitignore * pos matching progress * move file * rm comment * add velocities getter * fix bug * fix name bug * fix path bug * fix args func * add redshift calculation to catalogues * add shortcut to set n_sim and n_snap * if cond bug * add the cosine similarity * add verbosit iterator * add docs * update README * update README * update README 2022-11-25 10:44:08 +00:00			`build/*`
			`.eggs/*`
			`csiborgtools.egg-info/*`
Potential (#13) * add basic density field * Add TODO * add field smoothing * update how pos are calculated * add transforms both ways * add import * add sky density * add make skymap func * update TODO * update gitignore * add potential field calculation * delete boxsize setter * add tidal tensor 2022-11-27 07:53:38 +00:00			`Pylians3/*`
Power spectrum stuff (#16) * add autok1d * update TODO * add basic cross pk * del blank line * fix small bugs * fix loop bug * rm nbs * edit docstring * Update TODO * get rid of verbose flag * take all ICs * attempt better memory * simplify ASCII dump * rm verbose statement to get rid of bugs! * close fortran files * add MAS options * add boxsize setter * Move comment up * paths chagne * Update TODO * Update TODO * Forgotten units in Xpk * Attempt at fixing the distance bug * Update TODO * Update TODO * Remove comment * add summary reader * Update gitignore 2022-12-12 14:42:44 +00:00			`scripts/plot_correlation.ipynb`
kNN-CDF secondary halo bias (#40) * Add seperate autoknn script & config file * edit ics * Edit submission script * Add threshold values * Edit batch sizign * Remove print * edit * Rename files * Rename * Update nb * edit runs * Edit submit * Add median threshold * add new auto reader * editt submit * edit submit * Edit submit * Add mean prk * Edit runs * Remove correlation file * Move split to clutering * Add init * Remove import * Add the file * Add correlation reading * Edit scripts * Add below and above median permutation for cross * Update imports * Move rvs_in_sphere * Create utils * Split * Add import * Add normalised marks * Add import * Edit readme * Clean up submission file * Stop tracking submit files * Update gitignore * Add poisson field analytical expression * Add abstract generators * Add generators * Pass in the generator * Add a check for if there are any files * Start saving average density * Update nb * Update readme * Update units * Edit jobs * Update submits * Update reader * Add random crossing * Update crossing script * Add crossing with random * Update readme * Update notebook 2023-04-09 19:57:05 +00:00			`scripts/*.sh`
Add cleaner paths (#43) * ignore venv * ignore pylians if unavaible * Edit loading paths * Edit paths * Stop having default paths * Add nb * Add glamdring paths --------- Co-authored-by: Richard Stiskalek <dc-stis1@login8b.pri.cosma7.alces.network> Co-authored-by: Richard Stiskalek <dc-stis1@login8a.pri.cosma7.alces.network> 2023-04-14 22:24:52 +00:00			`venv/`
Add mmain and other major updates (#44) * Move paths to a separate file * Add mmain reader * Add a verbosity flag * Fix imports * Fix bug * Rename files * Return ultimate parents * Add script to generate mmain * Remove mmain path * edit path * Add mmain path * Change function name * Rename function * Turn off verbose * Fix list requirement * Edit init match paths * Fix init pathing * Edit paths docs * Edit dumpdir name * Rename path * Fix split paths * Remove unused import * Add comment * Update readme * remove read mmain * Rename haloatalogue * Fix minor bugs * Update nbs * Add create directory option * Move split jobs * Move spliot jobs * Remove splitting * Add import * Edit script * Deeper split folder * Fix paths bug * Rename catalogue * Rename Catalogue * Add new clumpread * Edit paths * add knn paths * Update commenting * Update imports * Add more conversions * Update temp file * Add a note * Add catalogue * Cooment * Update TODO * Update script * add nb * Update * pep8 * edit paths & pep8 * Fix knn auto paths * add paths docs * Add auto and cross knn paths * Add new paths * Simplify tpcf reading * pep8 patch * update readme * Update progress * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * pep8 * Pep 8 and restructure * add lambda spin * add clump and halo * add checks * Edit halo profile fit * Update gitignore * backup script 2023-04-18 09:02:36 +00:00			`.trunk/*`
Quijote kNN adding (#62) * Fix small bug * Add fiducial observers * Rename 1D knn * Add new bounds system * rm whitespace * Add boudns * Add simname to paths * Add fiducial obserevrs * apply bounds only if not none * Add TODO * add simnames * update script * Fix distance bug * update yaml * Update file reading * Update gitignore * Add plots * add check if empty list * add func to obtaining cross * Update nb * Remove blank lines * update ignroes * loop over a few ics * update gitignore * add comments 2023-05-15 22:30:10 +00:00			`scripts_test/`
			`scripts_plots/python.sh`
			`scripts_plots/submit.sh`
			`scripts_plots/*.out`
Add better diagnostics & plotting (#67) * Add caching functions * Add limts * Add new mass runs * Update .gitignore * Edit which CDFs are loaded * Stop saving cross hindxs * Change dist to half precision * New nearest path * Add neighbour counting * Add neighbour kwargs * Update work in progress * Add new counting * Add how dist is built * Collect dist to 1 file * Update reading routine * Delete Quijote files * Remove file * Back to float32 * Fix bugs * Rename utils * Remove neighbuor kwargs * Rename file * Fix bug * Rename plt utils * Change where nghb kwargs from * line length * Remove old notebooks * Move survey * Add white space * Update TODO * Update CDF calculation * Update temporarily plotting * Merge branch 'add_diagnostics' of github.com:Richard-Sti/csiborgtools into add_diagnostics * Start adding documentation to plotting * Remove comments * Better code documentation * Some work on tidal tensor * Better plotting * Add comment * Remove nb * Remove comment * Add documentation * Update plotting * Update submission * Update KL vs KS plots * Update the plotting routine * Update plotting * Update plotting routines 2023-06-16 13:33:27 +00:00			`scripts_plots/*.sh`
CSiBORG FoF switch (#75) * Add moving FoF membership files * add FoF membership path * Add notes where its PHEW * Add FoF catalogue path * Correct typo * Add more functionalities * Make work with halo IDs from FoF * Edit print statement * Fix copy bug * copy * Add FoF catalogue reading * Clean up script * Fix typo * Little edits * Fix naming convention * Rename key * Remove loading substructure particles * Rename CSiBORG Cat * Rename clumps cat * Rename cat * Remove misplaced import * Switch to halos * rm import * structfit of only halos * Add FoF halo reading * Add a short comment * Fix __getitem__ to work with int * Fix problems * Improve __getitem__ * Add more conversion * Fix indexing * Fix __getitem__ assertion * Fix numbers * Rename * Fix verbosity flags * Add full Quijote HMF option * Add plot of Quijote only * Add quijote full paths * Fix the fit_init script * Renam arg * Update .gitignore * add default argument name * Change default verbosity flag * Modernise script structure * Fix dictionary * Fix reading to include m200c * Modernise script * Add args 2023-07-24 12:10:21 +00:00			`notebooks/test.ipynb`
Add pynbody and other support (#92) * Simplify box units * Move old scripts * Add printing * Update readers * Disable boundscheck * Add new ordering * Clean up imports * Enforce dtype and add mass to quijote * Simplify print statements * Fix little typos * Fix key bug * Bug fixing * Delete boring comments * Improve ultimate clumps for PHEW * Delete boring comments * Add basic reading * Remove 0th index HID * Add flipping of X and Z * Updates to halo catalogues * Add ordered caching * Fix flipping * Add new flags * Fix PHEW empty clumps * Stop over-wrriting * Little improvements to angular neighbours * Add catalogue masking * Change if-else statements * Cache only filtered data * Add PHEW cats * Add comments * Sort imports * Get Quijote workign * Docs * Add HMF calculation * Move to old * Fix angular * Add great circle distance * Update imports * Update impotrts * Update docs * Remove unused import * Fix a quick bug * Update compatibility * Rename files * Renaming * Improve compatiblity * Rename snapsht * Fix snapshot bug * Update interface * Finish updating interface * Update all paths * Add old scripts * Add basic halo * Update imports * Improve snapshot processing * Update ordering * Fix how CM positions accessed * Add merger paths * Add imports * Add merger reading * Add making a merger tree * Add a basic merger tree reader * Add imports * Add main branch walking + comments + debuggin * Get tree running * Add working merger tree walking along main branch * Add units conversion for merger data * Add hid_to_array_index * Update merger tree * Add mergertree mass to PHEWcat * Edit comments * Add this to track changes... * Fix a little bug * Add mergertree mass * Add cache clearing * Improve summing substructure code * Littbe bug * Little updates to the merger tree reader * Update .giignore * Add box selection * Add optional deletingf of a group * add to keep track of changes * Update changes * Remove * Add manual tracker * Fix bug * Add m200c_to_r200c * Add manual halo tracking * Remove skipped snapshots * update cosmo params to match csiborg * remove old comments * Add SDSSxALFALFA * Fix bugs * Rename * Edit paths * Updates * Add comments * Add comment * Add hour conversion * Add imports * Add new observation class * Add selection * Add imports * Fix small bug * Add field copying for safety * Add matching to survey without masking * Add P(k) calculation * Add nb * Edit comment * Move files * Remove merger import * Edit setup.yp * Fix typo * Edit import warnigns * update nb * Update README * Update README * Update README * Add skeleton * Add skeleton 2023-12-07 14:23:32 +00:00			`scripts/mgtree.py`
			`scripts/makemerger.py`
Add density field plot and start preparing CSiBORG2 (#94) * Add RAMSES2HDF5 conversion * Upload changes * Clean up * More clean up * updates * Little change * pep9 * Add basic SPH calculation for a snapshot * Add submit script * Remove echo * Little changes * Send off changes * Little formatting * Little updates * Add nthreads argument * Upload chagnes * Add nthreads arguemnts * Some local changes.. * Update scripts * Add submission script * Update script * Update params * Rename CSiBORGBox to CSiBORG1box * Rename CSiBORG1 reader * Move files * Rename folder again * Add basic plotting here * Add new skeletons * Move def * Update nbs * Edit directories * Rename files * Add units to converted snapshots * Fix empty dataset bug * Delete file * Edits to submission scripts * Edit paths * Update .gitignore * Fix attrs * Update weighting * Fix RA/dec bug * Add FORNAX cluster * Little edit * Remove boxes since will no longer need * Move func back * Edit to include sort by membership * Edit paths * Purge basic things * Start removing * Bring file back * Scratch * Update the rest * Improve the entire file * Remove old things * Remove old * Delete old things * Fully updates * Rename file * Edit submit script * Little things * Add print statement * Add here cols_to_structured * Edit halo cat * Remove old import * Add comment * Update paths manager * Move file * Remove file * Add chains 2023-12-13 16:08:25 +00:00
			`*.out`
			`*/python.sh`
Sorting of CSiBORG2 initial snapshot (#99) * Attempt at the sorting script * Fix bug in CSiBORG2 sorting * and check sstatement * Simplify paths * Improve paths too * Update .gitignroe * Just rewrite commands.. 2023-12-20 10:00:26 +00:00			`scripts_independent/clear.sh`