Tutorial issues

[mctcampb]

Hi there, I am pretty new to using halotools, so I am trying trying to get a sense of the package by working through some of the available tutorials. I have downloaded the default halo catalogs and am working through the tutorial "Galaxy Catalog Analysis Example: Galaxy-galaxy lensing." However, when I copy and paste the first chunk of code into my notebook and try to run it, I get the following error: 'CachedHaloCatalog' object has no attribute '_halo_table'. I have also downloaded some of the jupyter notebooks from the documents section and tried to run them myself, and the same error message popped up. I would really appreciate any help!

[aphearin]

Hi @mctcampb before running the notebook, did you first download the initial halo catalog data? There are docs for that in the Getting Started with Halotools quickstart guide. In case you did not, then I think this error is expected.

[mctcampb]

Hi there,

Yes, I have downloaded every available halo catalog. Other members of my team are experiencing the same issue, and cannot use certain catalogs.

[aphearin]

Hi @mctcampb sorry this issue continues to cause you problems. I have been having trouble reproducing it and so I'm having a hard time figuring out what could be causing it. When I run the first code cell of this notebook locally on my machine, it executes without complaints. The only things I can think of that would cause what you are seeing would be that either there was some problem with the download of the halo catalog, or that it has not been cached. Are you able to confirm that you do indeed have the halo table on disk? If you used the download_additional_halocat.py script that ships with halotools, then your halo catalog would be stored here:

$HOME/.astropy/cache/halotools/halo_catalogs/bolshoi/rockstar

There should also be a corresponding entry in the halo catalog cache log, which should be located here:
$HOME/.astropy/cache/halotools/halo_table_cache_log.txt

If you inspect that file (which is just plain ASCII), you should see an entry for every one of the halo catalogs you downloaded and cached, along with the path where it is stored. Could you check on these two things and let me know what you find?

[mctcampb]

Hi there, it seems like we figured out the issue. This problem only appears when using Windows, but not Linux/macOS. Thank you for the help!

[cmlamman]

I ran into the same problem after installing halotools 9.0 on Windows 11 via conda. Apparently clean install and I correctly prepped the cached halo catalogs, but they didn't always work in the tutorials. If helpful, I've copied the full error message I got when running the third cell of hod_modeling_tutorial_with_alignments.ipynb :

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
File c:\ProgramData\miniconda3\Lib\site-packages\halotools\sim_manager\cached_halo_catalog.py:543, in CachedHaloCatalog.halo_table(self)
    [542](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:542) try:
--> [543](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:543)     return self._halo_table
    [544](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:544) except AttributeError:

AttributeError: 'CachedHaloCatalog' object has no attribute '_halo_table'

During handling of the above exception, another exception occurred:

AssertionError                            Traceback (most recent call last)
File c:\ProgramData\miniconda3\Lib\site-packages\halotools\utils\crossmatch.py:143, in crossmatch(x, y, skip_bounds_checking)
    [142](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/crossmatch.py:142) assert len(set(y)) == len(y)
--> [143](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/crossmatch.py:143) assert np.all(np.array(y).astype(int) == y)
    [144](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/crossmatch.py:144) assert np.shape(y) == (len(y),)

AssertionError: 

During handling of the above exception, another exception occurred:

ValueError                                Traceback (most recent call last)
Cell In[3], [line 2](vscode-notebook-cell:?execution_count=3&line=2)
      [1](vscode-notebook-cell:?execution_count=3&line=1) halocat = CachedHaloCatalog(simname='bolplanck', halo_finder='rockstar', redshift=0, version_name='halotools_v0p4')
----> [2](vscode-notebook-cell:?execution_count=3&line=2) mask_bad_halocat(halocat)

Cell In[2], [line 3](vscode-notebook-cell:?execution_count=2&line=3)
      [2](vscode-notebook-cell:?execution_count=2&line=2) def mask_bad_halocat(halocat):
----> [3](vscode-notebook-cell:?execution_count=2&line=3)     bad_mask = (halocat.halo_table["halo_axisA_x"] == 0) & (halocat.halo_table["halo_axisA_y"] == 0) & (halocat.halo_table["halo_axisA_z"] == 0)
      [4](vscode-notebook-cell:?execution_count=2&line=4)     halocat._halo_table = halocat.halo_table[ ~bad_mask ]

File c:\ProgramData\miniconda3\Lib\site-packages\halotools\sim_manager\cached_halo_catalog.py:547, in CachedHaloCatalog.halo_table(self)
    [545](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:545) if self.log_entry.safe_for_cache is True:
    [546](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:546)     self._halo_table = Table.read(_passively_decode_string(self.fname), path='data')
--> [547](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:547)     self._add_new_derived_columns(self._halo_table)
    [548](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:548)     return self._halo_table
    [549](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:549) else:

File c:\ProgramData\miniconda3\Lib\site-packages\halotools\sim_manager\cached_halo_catalog.py:557, in CachedHaloCatalog._add_new_derived_columns(self, t)
    [554](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:554)     add_halo_hostid(t)
    [556](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:556) if 'halo_mvir_host_halo' not in list(t.keys()):
--> [557](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/sim_manager/cached_halo_catalog.py:557)     broadcast_host_halo_property(t, 'halo_mvir')

File c:\ProgramData\miniconda3\Lib\site-packages\halotools\utils\value_added_halo_table_functions.py:83, in broadcast_host_halo_property(table, halo_property_key, delete_possibly_existing_column)
     [78](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/value_added_halo_table_functions.py:78) elif (new_colname in list(table.keys())) & (
     [79](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/value_added_halo_table_functions.py:79)     delete_possibly_existing_column is True
     [80](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/value_added_halo_table_functions.py:80) ):
     [81](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/value_added_halo_table_functions.py:81)     del table[new_colname]
---> [83](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/value_added_halo_table_functions.py:83) idx_halos, idx_hosts = crossmatch(table["halo_hostid"].data, table["halo_id"].data)
     [84](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/value_added_halo_table_functions.py:84) table[new_colname] = np.zeros(len(table), dtype=table[halo_property_key].dtype)
     [85](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/value_added_halo_table_functions.py:85) table[new_colname][idx_halos] = table[halo_property_key][idx_hosts]

File c:\ProgramData\miniconda3\Lib\site-packages\halotools\utils\crossmatch.py:147, in crossmatch(x, y, skip_bounds_checking)
    [145](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/crossmatch.py:145) except:
    [146](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/crossmatch.py:146)     msg = "Input array y must be a 1d sequence of unique integers"
--> [147](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/crossmatch.py:147)     raise ValueError(msg)
    [148](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/crossmatch.py:148) try:
    [149](file:///C:/ProgramData/miniconda3/Lib/site-packages/halotools/utils/crossmatch.py:149)     assert np.all(np.array(x).astype(int) == x)

ValueError: Input array y must be a 1d sequence of unique integers
/media/nvanalfen/T7/Northeastern/Research/my halotools/halotools/halotools/empirical_models/ia_models/ia_model_components.py:190: UserWarning: `central_alignment_strength` not detected in the table, using value in self.param_dict.
  warn(msg)
/media/nvanalfen/T7/Northeastern/Research/my halotools/halotools/halotools/empirical_models/ia_models/ia_model_components.py:520: UserWarning: `satellite_alignment_strength` key not detected in `table`.The value set in self.param_dict of this class will be used instead.
  warn(msg)