astroARIADNE Requirements from setup.py not being correctly installed

Requirements from setup.py not being correctly installed

Open jgagneastro opened this issue 7 months ago • 0 comments
I do not understand why exactly, but installing from the GitHub repo's setup.py in a fresh conda environment does not automatically install all required packages (tqdm in particular is missing). This is strange because "tqdm" is listed in setup.py, but it would be worth trying to reproduce and fix this problem. Maybe it's related to the deprecation warnings about "setup.py".
The full outputs from a fresh conda env can be found below:
(base) Mizar jonathan jonathan $ conda create --name ariadne4 python
Channels:
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /opt/anaconda3-native/anaconda3/envs/ariadne4

  added / updated specs:
    - python


The following NEW packages will be INSTALLED:

  bzip2              conda-forge/osx-arm64::bzip2-1.0.8-h99b78c6_7 
  ca-certificates    conda-forge/osx-arm64::ca-certificates-2024.7.4-hf0a4a13_0 
  libexpat           conda-forge/osx-arm64::libexpat-2.6.2-hebf3989_0 
  libffi             conda-forge/osx-arm64::libffi-3.4.2-h3422bc3_5 
  libsqlite          conda-forge/osx-arm64::libsqlite-3.46.0-hfb93653_0 
  libzlib            conda-forge/osx-arm64::libzlib-1.3.1-hfb2fe0b_1 
  ncurses            conda-forge/osx-arm64::ncurses-6.5-hb89a1cb_0 
  openssl            conda-forge/osx-arm64::openssl-3.3.1-hfb2fe0b_1 
  pip                conda-forge/noarch::pip-24.0-pyhd8ed1ab_0 
  python             conda-forge/osx-arm64::python-3.12.4-h30c5eda_0_cpython 
  readline           conda-forge/osx-arm64::readline-8.2-h92ec313_1 
  setuptools         conda-forge/noarch::setuptools-70.3.0-pyhd8ed1ab_0 
  tk                 conda-forge/osx-arm64::tk-8.6.13-h5083fa2_1 
  tzdata             conda-forge/noarch::tzdata-2024a-h0c530f3_0 
  wheel              conda-forge/noarch::wheel-0.43.0-pyhd8ed1ab_1 
  xz                 conda-forge/osx-arm64::xz-5.2.6-h57fd34a_0 


Proceed ([y]/n)? y


Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate ariadne4
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) Mizar jonathan jonathan $ conda activate ariadne4
(ariadne4) Mizar jonathan jonathan $ python
Python 3.12.4 | packaged by conda-forge | (main, Jun 17 2024, 10:13:44) [Clang 16.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> exit()
(ariadne4) Mizar jonathan jonathan $ pip install astroARIADNE
Collecting astroARIADNE
  Downloading astroARIADNE-1.1.1.tar.gz (56.0 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.0/56.0 MB 6.6 MB/s eta 0:00:00
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: astroARIADNE
  Building wheel for astroARIADNE (setup.py) ... done
  Created wheel for astroARIADNE: filename=astroARIADNE-1.1.1-py3-none-any.whl size=56199672 sha256=64f68fbabb5eb2bc8258a8172dfe1f6245ab9624469e158f3ffaeb15dafd0bd0
  Stored in directory: /Users/jonathan/Library/Caches/pip/wheels/96/37/9f/ab68948add9ccce7b9949fcb33e924dfbc91e88dff71ff4486
Successfully built astroARIADNE
Installing collected packages: astroARIADNE
Successfully installed astroARIADNE-1.1.1
(ariadne4) Mizar jonathan jonathan $ python
Python 3.12.4 | packaged by conda-forge | (main, Jun 17 2024, 10:13:44) [Clang 16.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from astroARIADNE.star import Star
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/jonathan/astroARIADNE/__init__.py", line 13, in <module>
    from .fitter import Fitter
  File "/Users/jonathan/astroARIADNE/fitter.py", line 10, in <module>
    from tqdm import tqdm
ModuleNotFoundError: No module named 'tqdm'
>>> exit()
(ariadne4) Mizar jonathan jonathan $ pip uninstall astroARIADNE
Found existing installation: astroARIADNE 1.1.1
Uninstalling astroARIADNE-1.1.1:
  Would remove:
    /opt/anaconda3-native/anaconda3/envs/ariadne4/lib/python3.12/site-packages/astroARIADNE-1.1.1.dist-info/*
    /opt/anaconda3-native/anaconda3/envs/ariadne4/lib/python3.12/site-packages/astroARIADNE/*
Proceed (Y/n)? y
  Successfully uninstalled astroARIADNE-1.1.1
(ariadne4) Mizar jonathan jonathan $ cd Downloads 
(ariadne4) Mizar jonathan Downloads $ mkdir astroariadne_again
(ariadne4) Mizar jonathan Downloads $ cd astroariadne_again
(ariadne4) Mizar jonathan astroariadne_again $ git clone https://github.com/jvines/astroARIADNE.git
cd astroARIADNE
Cloning into 'astroARIADNE'...
remote: Enumerating objects: 2167, done.
remote: Counting objects: 100% (352/352), done.
remote: Compressing objects: 100% (45/45), done.
remote: Total 2167 (delta 327), reused 318 (delta 307), pack-reused 1815
Receiving objects: 100% (2167/2167), 59.57 MiB | 6.72 MiB/s, done.
Resolving deltas: 100% (1527/1527), done.
(ariadne4) Mizar jonathan (master) astroARIADNE $ python setup.py install 
running install
/opt/anaconda3-native/anaconda3/envs/ariadne4/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` directly.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
        ********************************************************************************

!!
  self.initialize_options()
/opt/anaconda3-native/anaconda3/envs/ariadne4/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

        ********************************************************************************
        Please avoid running ``setup.py`` and ``easy_install``.
        Instead, use pypa/build, pypa/installer or other
        standards-based tools.

        See https://github.com/pypa/setuptools/issues/917 for details.
        ********************************************************************************

!!
  self.initialize_options()
running bdist_egg
running egg_info
creating astroARIADNE.egg-info
writing astroARIADNE.egg-info/PKG-INFO
writing dependency_links to astroARIADNE.egg-info/dependency_links.txt
writing top-level names to astroARIADNE.egg-info/top_level.txt
writing manifest file 'astroARIADNE.egg-info/SOURCES.txt'
reading manifest file 'astroARIADNE.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'astroARIADNE.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-11.0-arm64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/astroARIADNE
copying astroARIADNE/config.py -> build/lib/astroARIADNE
copying astroARIADNE/error.py -> build/lib/astroARIADNE
copying astroARIADNE/phot_utils.py -> build/lib/astroARIADNE
copying astroARIADNE/sed_library.py -> build/lib/astroARIADNE
copying astroARIADNE/isochrone.py -> build/lib/astroARIADNE
copying astroARIADNE/librarian.py -> build/lib/astroARIADNE
copying astroARIADNE/star.py -> build/lib/astroARIADNE
copying astroARIADNE/__init__.py -> build/lib/astroARIADNE
copying astroARIADNE/plotter.py -> build/lib/astroARIADNE
copying astroARIADNE/utils.py -> build/lib/astroARIADNE
copying astroARIADNE/fitter.py -> build/lib/astroARIADNE
creating build/lib/astroARIADNE/Datafiles
copying astroARIADNE/Datafiles/Template_prior.dat -> build/lib/astroARIADNE/Datafiles
copying astroARIADNE/Datafiles/mamajek_spt.dat -> build/lib/astroARIADNE/Datafiles
copying astroARIADNE/Datafiles/model_grid_fix.dat -> build/lib/astroARIADNE/Datafiles
copying astroARIADNE/Datafiles/plot_settings.dat -> build/lib/astroARIADNE/Datafiles
creating build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/BTCond_DF.pkl -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/BTNextGen_DF.pkl -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/BTSettl_DF.pkl -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/CK04_DF.pkl -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/Coelho_DF.pkl -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/Kurucz_DF.pkl -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/Phoenixv2_DF.pkl -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/model_grid_BT_Cond.dat -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/model_grid_BT_NextGen.dat -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/model_grid_BT_Settl.dat -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/model_grid_CK04.dat -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/model_grid_Coelho.dat -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/model_grid_Kurucz.dat -> build/lib/astroARIADNE/Datafiles/model_grids
copying astroARIADNE/Datafiles/model_grids/model_grid_Phoenixv2.dat -> build/lib/astroARIADNE/Datafiles/model_grids
creating build/lib/astroARIADNE/Datafiles/prior
copying astroARIADNE/Datafiles/prior/logg_kde.pkl -> build/lib/astroARIADNE/Datafiles/prior
copying astroARIADNE/Datafiles/prior/logg_ppf.pkl -> build/lib/astroARIADNE/Datafiles/prior
copying astroARIADNE/Datafiles/prior/teff_kde.pkl -> build/lib/astroARIADNE/Datafiles/prior
copying astroARIADNE/Datafiles/prior/teff_ppf.pkl -> build/lib/astroARIADNE/Datafiles/prior
copying astroARIADNE/Datafiles/prior/z_logg_kde.pkl -> build/lib/astroARIADNE/Datafiles/prior
creating build/bdist.macosx-11.0-arm64
creating build/bdist.macosx-11.0-arm64/egg
creating build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/config.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/error.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/phot_utils.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/sed_library.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/isochrone.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/librarian.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/star.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/__init__.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/plotter.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
copying build/lib/astroARIADNE/utils.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
creating build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles
copying build/lib/astroARIADNE/Datafiles/mamajek_spt.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles
copying build/lib/astroARIADNE/Datafiles/Template_prior.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles
copying build/lib/astroARIADNE/Datafiles/plot_settings.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles
creating build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/model_grid_Kurucz.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/Phoenixv2_DF.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/model_grid_BT_Cond.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/model_grid_BT_NextGen.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/CK04_DF.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/model_grid_BT_Settl.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/BTCond_DF.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/model_grid_Coelho.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/BTNextGen_DF.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/Kurucz_DF.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/Coelho_DF.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/model_grid_CK04.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/model_grid_Phoenixv2.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grids/BTSettl_DF.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/model_grids
copying build/lib/astroARIADNE/Datafiles/model_grid_fix.dat -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles
creating build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/prior
copying build/lib/astroARIADNE/Datafiles/prior/teff_kde.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/prior
copying build/lib/astroARIADNE/Datafiles/prior/teff_ppf.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/prior
copying build/lib/astroARIADNE/Datafiles/prior/z_logg_kde.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/prior
copying build/lib/astroARIADNE/Datafiles/prior/logg_kde.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/prior
copying build/lib/astroARIADNE/Datafiles/prior/logg_ppf.pkl -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE/Datafiles/prior
copying build/lib/astroARIADNE/fitter.py -> build/bdist.macosx-11.0-arm64/egg/astroARIADNE
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/config.py to config.cpython-312.pyc
build/bdist.macosx-11.0-arm64/egg/astroARIADNE/config.py:62: SyntaxWarning: invalid escape sequence '\m'
  __bibtex__ = '''
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/error.py to error.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/phot_utils.py to phot_utils.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/sed_library.py to sed_library.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/isochrone.py to isochrone.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/librarian.py to librarian.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/star.py to star.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/__init__.py to __init__.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/plotter.py to plotter.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/utils.py to utils.cpython-312.pyc
byte-compiling build/bdist.macosx-11.0-arm64/egg/astroARIADNE/fitter.py to fitter.cpython-312.pyc
creating build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying astroARIADNE.egg-info/PKG-INFO -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying astroARIADNE.egg-info/SOURCES.txt -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying astroARIADNE.egg-info/dependency_links.txt -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
copying astroARIADNE.egg-info/top_level.txt -> build/bdist.macosx-11.0-arm64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
astroARIADNE.__pycache__.config.cpython-312: module MAY be using inspect.getfile
creating dist
creating 'dist/astroARIADNE-1.1.1-py3.12.egg' and adding 'build/bdist.macosx-11.0-arm64/egg' to it
removing 'build/bdist.macosx-11.0-arm64/egg' (and everything under it)
Processing astroARIADNE-1.1.1-py3.12.egg
creating /opt/anaconda3-native/anaconda3/envs/ariadne4/lib/python3.12/site-packages/astroARIADNE-1.1.1-py3.12.egg
Extracting astroARIADNE-1.1.1-py3.12.egg to /opt/anaconda3-native/anaconda3/envs/ariadne4/lib/python3.12/site-packages
/opt/anaconda3-native/anaconda3/envs/ariadne4/lib/python3.12/site-packages/astroARIADNE-1.1.1-py3.12.egg/astroARIADNE/config.py:62: SyntaxWarning: invalid escape sequence '\m'
  __bibtex__ = '''
Adding astroARIADNE 1.1.1 to easy-install.pth file

Installed /opt/anaconda3-native/anaconda3/envs/ariadne4/lib/python3.12/site-packages/astroARIADNE-1.1.1-py3.12.egg
Processing dependencies for astroARIADNE==1.1.1
Finished processing dependencies for astroARIADNE==1.1.1
(ariadne4) Mizar jonathan (master) astroARIADNE $ python
Python 3.12.4 | packaged by conda-forge | (main, Jun 17 2024, 10:13:44) [Clang 16.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from astroARIADNE.star import Star
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/jonathan/Downloads/astroariadne_again/astroARIADNE/astroARIADNE/__init__.py", line 13, in <module>
    from .fitter import Fitter
  File "/Users/jonathan/Downloads/astroariadne_again/astroARIADNE/astroARIADNE/fitter.py", line 10, in <module>
    from tqdm import tqdm
ModuleNotFoundError: No module named 'tqdm'
>>>
Jul 16 '24 13:07 jgagneastro
astroARIADNE astroARIADNE copied to clipboard

Requirements from setup.py not being correctly installed

astroARIADNE
astroARIADNE copied to clipboard
