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

setup.py

@@ -1,52 +1,28 @@
 from setuptools import find_packages, setup
 
-# List of dependencies:
-#   - Corrfunc  -> To be moved to a separate package.
-#   - NumPy
-#   - SciPy
-#   - Numba
-#   - Pylians
-#   - tqdm
-#   - healpy
-#   - astropy
-#   - scikit-learn
-#   - joblib
-#   - h5py
-#   - MPI
-#   - pyyaml
-#   - taskmaster
-#   - matplotlib
-#   - scienceplots
-#   - cache_to_disk
-
-
 BUILD_REQ = ["numpy", "scipy"]
 INSTALL_REQ = BUILD_REQ
-INSTALL_REQ += ["Corrfunc",
-                "Pylians",
+INSTALL_REQ += [
                 "numba",
                 "tqdm",
                 "healpy",
                 "astropy",
                 "scikit-learn",
                 "h5py",
-                "matplotlib",
-                "scienceplots",
-                "mpi4py",
-                "pyyaml",
-                "joblib",]
-
+                "pynbody",
+                "joblib",
+                ]
 
 setup(
     name="csiborgtools",
-    version="0.2",
+    version="0.3",
     description="CSiBORG analysis tools",
     url="https://github.com/Richard-Sti/csiborgtools",
     author="Richard Stiskalek",
     author_email="richard.stiskalek@protonmail.com",
     license="GPL-3.0",
     packages=find_packages(),
-    python_requires=">=3.8",
+    python_requires=">=3.6",
     build_requires=BUILD_REQ,
     setup_requires=BUILD_REQ,
     install_requires=INSTALL_REQ,
@@ -55,5 +31,6 @@ setup(
         "Intended Audience :: Science/Research",
         "Operating System :: POSIX :: Linux",
         "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9"]
+        "Programming Language :: Python :: 3.9"
+        ]
 )