Merge pull request #20 from SWIFTSIM/update_deps

Update dependencies

Author: kyleaoman

README.rst

@@ -14,15 +14,10 @@ SWIFTGalaxy
 
 SWIFTGalaxy is a module that extends SWIFTSimIO_ tailored to analyses of particles belonging to individual simulated galaxies. It inherits from and extends the functionality of the ``SWIFTDataset``. It understands the content of halo catalogues (supported: `Velociraptor`_, `Caesar`_, `SOAP`_) and therefore which particles belong to a galaxy or other group of particles, and its integrated properties. The particles occupy a coordinate frame that is enforced to be consistent, such that particles loaded on-the-fly will match e.g. rotations and translations of particles already in memory. Intuitive masking of particle datasets is also enabled. Finally, some utilities to make working in cylindrical and spherical coordinate systems more convenient are also provided.
 
-.. warning::
-
-   In order to support use of SOAP halo catalogues this version (1.1.0) of SWIFTGalaxy depends on the `load_fof_catalogues`_ branch of SWIFTSimIO. This dependency will be automatically handled by ``pip``, but to use SOAP catalogues in SWIFTGalaxy you **must** install from github. One way to do this is ``pip install git+https://github.com/SWIFTSIM/swiftgalaxy.git``. PyPI_ does not allow depending on github repositories so SWIFTGalaxy v1.1.0 will not be released on PyPI (and therefore cannot be installed with ``pip install swiftgalaxy``) until the load_fof_catalogues branch is merged into SWIFTSimIO and itself released on PyPI. You can use the PyPI versions of both SWIFTGalaxy and SWIFTSimIO (these are compatible) but in this case SOAP halo catalogues are not supported.
-
 .. _SWIFTSimIO: http://swiftsimio.readthedocs.org
 .. _Velociraptor: https://ui.adsabs.harvard.edu/abs/2019PASA...36...21E/abstract
 .. _Caesar: https://caesar.readthedocs.io/en/latest/
 .. _SOAP: https://github.com/SWIFTSIM/SOAP
-.. _load_fof_catalogues: https://github.com/SWIFTSIM/swiftsimio/tree/load_fof_catalogues
 .. _PyPI: https://pypi.org
 
 .. INTRO_END_LABEL

docs/source/halo_catalogues/index.rst

@@ -16,11 +16,6 @@ The `SOAP`_ catalogue format is the preferred catalogue format of the `SWIFT com
 
 .. _SWIFT community: https://github.com/SWIFTSIM
 .. _SOAP: https://github.com/SWIFTSIM/SOAP
-.. _load_fof_catalogues: https://github.com/SWIFTSIM/swiftsimio/tree/load_fof_catalogues
-
-.. warning ::
-
-   At the time of writing :mod:`swiftsimio` support for reading SOAP catalogues is functional but still under active development. The ``master`` branch of the :mod:`swiftsimio` repository does not yet allow reading SOAP catalogues. To use :mod:`swiftgalaxy` with SOAP catalogues currently requires installing the `load_fof_catalogues`_ branch of :mod:`swiftsimio`. One way to do this is ``pip install git+https://github.com/SWIFTSIM/swiftsimio.git@load_fof_catalogues``.
 
 Setting up an instance of the helper class is straightforward. We'll assume a SOAP catalogue called :file:`halo_properties_0123.hdf5`, and suppose that we're interested in the first object in the catalogue (row ``0``):
 

examples/SWIFTGalaxy_Colibre_QuickStart.ipynb

@@ -264,7 +264,8 @@
    "source": [
     "for ptype in \"gas\", \"dark_matter\", \"stars\":\n",
     "    getattr(sg, ptype).smoothing_length = generate_smoothing_lengths(\n",
-    "        (getattr(sg, ptype).coordinates + sg.centre) % sg.metadata.boxsize,  # modified to wrap the box\n",
+    "        (getattr(sg, ptype).coordinates + sg.centre)\n",
+    "        % sg.metadata.boxsize,  # modified to wrap the box\n",
     "        sg.metadata.boxsize,\n",
     "        kernel_gamma=1.8,\n",
     "        neighbours=57,\n",
@@ -623,7 +624,7 @@
     "            # no particles of this type\n",
     "            print(f\"no {ptype}\")\n",
     "    myvis(sg, fignum=figcounter)\n",
-    "    figcounter += 1\n"
+    "    figcounter += 1"
    ]
   }
  ],

optional_requirements.txt

@@ -1,5 +1,5 @@
 pytest
 black[jupyter]
 wily
-git+https://github.com/kyleaoman/velociraptor-python.git@load_fof_catalogues
+velociraptor
 git+https://github.com/dnarayanan/caesar.git

requirements.txt

@@ -2,5 +2,5 @@ numpy
 scipy
 h5py
 unyt
-git+https://github.com/SWIFTSIM/swiftsimio.git
+swiftsimio
 astropy