Numba version in lock file calls function from later version

[chrisfrohmaier]

Describe the bug
The numba version in the latest lock file is 0.53.1 but code calls from numba.np.ufunc.parallel import get_thread_id, get_num_threads. The function get_thread_id doesn't exist in this version. I have numba==0.57.1 for another project in a different environment and am able to import the get_thread_id function.

To Reproduce
Follow the installation instructions to a fresh environment using the latest lock file: https://tardis-sn.github.io/tardis/installation.html
I installed using pip
I followed the quickstart tutorial https://tardis-sn.github.io/tardis/quickstart.html
Failed on Cell 6

sim = run_tardis("tardis_example.yml",
                 virtual_packet_logging=True,
                 show_convergence_plots=True,
                 export_convergence_plots=True,
                 log_level="INFO")

Error message:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[6], line 1
----> 1 sim = run_tardis("tardis_example.yml",
      2                  virtual_packet_logging=True,
      3                  show_convergence_plots=True,
      4                  export_convergence_plots=True,
      5                  log_level="INFO")

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/base.py:76, in run_tardis(config, atom_data, packet_source, simulation_callbacks, virtual_packet_logging, show_convergence_plots, log_level, specific_log_level, show_progress_bars, **kwargs)
     74 from tardis.io.configuration.config_reader import Configuration
     75 from tardis.io.atom_data.base import AtomData
---> 76 from tardis.simulation import Simulation
     78 if isinstance(config, Configuration):
     79     tardis_config = config

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/simulation/__init__.py:5
      1 """
      2 Handling simulation runs.
      3 """
----> 5 from tardis.simulation.base import Simulation

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/simulation/base.py:9
      7 from tardis import constants as const
      8 from collections import OrderedDict
----> 9 from tardis import model
     11 from tardis.montecarlo.base import MontecarloTransport
     12 from tardis.model import SimulationState

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/model/__init__.py:9
      1 """
      2 Holding information about the TARDIS model.
      3
   (...)
      6 factor of the model used in the simulation.
      7 """
----> 9 from tardis.model.base import *

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/model/base.py:32
     25 from tardis.io.decay import IsotopeAbundances
     27 from tardis.io.model.parse_density_configuration import (
     28     parse_config_v1_density,
     29     parse_csvy_density,
     30     calculate_density_after_time,
     31 )
---> 32 from tardis.montecarlo.packet_source import BlackBodySimpleSource
     34 from tardis.radiation_field.base import MonteCarloRadiationFieldState
     36 logger = logging.getLogger(__name__)

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/montecarlo/__init__.py:10
      1 """
      2 Faciliating the MonteCarlo iterations.
      3
   (...)
      7 properties and with the last iteration, the spectrum is determined.
      8 """
---> 10 from tardis.montecarlo.base import *

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/montecarlo/base.py:17
     15 from tardis.io.util import HDFWriterMixin
     16 from tardis.montecarlo import packet_source as source
---> 17 from tardis.montecarlo.montecarlo_numba.formal_integral import FormalIntegrator
     18 from tardis.montecarlo import montecarlo_configuration as mc_config_module
     21 from tardis.montecarlo.montecarlo_numba import montecarlo_radial1d

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/montecarlo/montecarlo_numba/__init__.py:16
      9 njit_dict_no_parallel = {
     10     "fastmath": True,
     11     "error_model": "numpy",
     12     "parallel": False,
     13 }
     15 from tardis.montecarlo.montecarlo_numba.r_packet import RPacket
---> 16 from tardis.montecarlo.montecarlo_numba.base import montecarlo_radial1d
     17 from tardis.montecarlo.montecarlo_numba.numba_interface import PacketCollection

File ~/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/tardis/montecarlo/montecarlo_numba/base.py:2
      1 from numba import prange, njit, objmode
----> 2 from numba.np.ufunc.parallel import get_thread_id, get_num_threads
      4 import numpy as np
      6 from tardis.montecarlo.montecarlo_numba.r_packet import (
      7     RPacket,
      8     PacketStatus,
      9 )

ImportError: cannot import name 'get_thread_id' from 'numba.np.ufunc.parallel' (/home/cf5g09/anaconda3/envs/tardis_pip/lib/python3.8/site-packages/numba/np/ufunc/parallel.py)

System

• OS:

  • GNU/Linux
  • macOS

• Environment (conda list):

# packages in environment at /home/cf5g09/anaconda3/envs/tardis_pip:
#
# Name                    Version                   Build  Channel
_ipython_minor_entry_point 8.7.0                h3b92ee0_0    conda-forge
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alabaster                 0.7.13             pyhd8ed1ab_0    conda-forge
anyio                     4.0.0              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py38h0a891b7_3    conda-forge
arrow                     1.2.3              pyhd8ed1ab_0    conda-forge
astropy                   5.0.4            py38h71d37f0_0    conda-forge
astropy-sphinx-theme      1.1                pyhd8ed1ab_0    conda-forge
asttokens                 2.4.0              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
atk-1.0                   2.38.0               hd4edc92_1    conda-forge
attrs                     23.1.0             pyh71513ae_1    conda-forge
babel                     2.12.1             pyhd8ed1ab_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                pyhd8ed1ab_3    conda-forge
backports.functools_lru_cache 1.6.5              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.2             pyha770c72_0    conda-forge
black                     22.3.0             pyhd8ed1ab_0    conda-forge
bleach                    6.0.0              pyhd8ed1ab_0    conda-forge
blosc                     1.21.5               h0f2a231_0    conda-forge
brotli                    1.1.0                hd590300_0    conda-forge
brotli-bin                1.1.0                hd590300_0    conda-forge
brotli-python             1.1.0            py38h17151c0_0    conda-forge
brotlipy                  0.7.0           py38h0a891b7_1005    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.19.1               hd590300_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cairo                     1.16.0            h0c91306_1017    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py38h4a40e3a_3    conda-forge
charset-normalizer        3.2.0              pyhd8ed1ab_0    conda-forge
click                     8.1.7           unix_pyh707e725_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.1.4              pyhd8ed1ab_0    conda-forge
commonmark                0.9.1                      py_0    conda-forge
coverage                  7.3.1            py38h01eb140_0    conda-forge
cryptography              40.0.2           py38h3d167d9_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
dataclasses               0.8                pyhc8e2a94_3    conda-forge
debugpy                   1.8.0            py38h17151c0_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
docutils                  0.18.1           py38h578d9bd_1    conda-forge
dot2tex                   2.11.3             pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.1.3              pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
flit-core                 3.9.0              pyhd8ed1ab_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.42.1           py38h01eb140_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
fribidi                   1.0.10               h36c2ea0_0    conda-forge
future                    0.18.3             pyhd8ed1ab_0    conda-forge
gdk-pixbuf                2.42.10              h6c15284_3    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
giflib                    5.2.1                h0b41bf4_3    conda-forge
git-lfs                   3.4.0                ha770c72_0    conda-forge
gmp                       6.2.1                h58526e2_0    conda-forge
gmpy2                     2.1.2            py38h793c122_1    conda-forge
graphite2                 1.3.13            h58526e2_1001    conda-forge
graphviz                  8.1.0                h28d9a01_0    conda-forge
gtk2                      2.24.33              h90689f9_2    conda-forge
gts                       0.7.6                h977cf35_4    conda-forge
h5py                      3.7.0           nompi_py38h045baee_101    conda-forge
harfbuzz                  8.2.0                h3d44ed6_0    conda-forge
hdf5                      1.12.2          nompi_h4df4325_101    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
imagesize                 1.4.1              pyhd8ed1ab_0    conda-forge
importlib-metadata        6.8.0              pyha770c72_0    conda-forge
importlib_metadata        6.8.0                hd8ed1ab_0    conda-forge
importlib_resources       6.0.1              pyhd8ed1ab_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.25.2             pyh2140261_0    conda-forge
ipython                   8.12.2             pyh41d4057_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.8.0              pyhd8ed1ab_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.0             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
json5                     0.9.14             pyhd8ed1ab_0    conda-forge
jsonpointer               2.4              py38h578d9bd_2    conda-forge
jsonschema                4.19.0             pyhd8ed1ab_1    conda-forge
jsonschema-specifications 2023.7.1           pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.19.0             pyhd8ed1ab_1    conda-forge
jupyter-lsp               2.2.0              pyhd8ed1ab_0    conda-forge
jupyter_client            8.3.1              pyhd8ed1ab_0    conda-forge
jupyter_core              5.3.0            py38h578d9bd_0    conda-forge
jupyter_events            0.7.0              pyhd8ed1ab_2    conda-forge
jupyter_server            2.7.3              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyterlab                4.0.6              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_server         2.25.0             pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        1.1.7              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5            py38h7f3f72f_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
latexcodec                2.0.1              pyh9f0ad1d_0    conda-forge
lcms2                     2.15                 h7f713cb_2    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libaec                    1.0.6                hcb278e6_1    conda-forge
libblas                   3.9.0           18_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_0    conda-forge
libbrotlidec              1.1.0                hd590300_0    conda-forge
libbrotlienc              1.1.0                hd590300_0    conda-forge
libcblas                  3.9.0           18_linux64_openblas    conda-forge
libcurl                   8.3.0                hca28451_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_1    conda-forge
libgd                     2.3.3                he9388d3_8    conda-forge
libgfortran-ng            13.2.0               h69a702a_1    conda-forge
libgfortran5              13.2.0               ha4646dd_1    conda-forge
libglib                   2.78.0               hebfc3b9_0    conda-forge
libgomp                   13.2.0               h807b86a_1    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              hd590300_1    conda-forge
liblapack                 3.9.0           18_linux64_openblas    conda-forge
libllvm10                 10.0.1               he513fc3_3    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
librsvg                   2.56.3               h98fae49_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsqlite                 3.43.0               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_1    conda-forge
libtiff                   4.6.0                h8b53f26_0    conda-forge
libtool                   2.4.7                h27087fc_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp                   1.3.2                hdffd6e0_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libxslt                   1.1.37               h0054252_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
llvmlite                  0.36.0           py38h4630a5e_0    conda-forge
lxml                      4.9.3            py38h0ef1326_0    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
markupsafe                2.1.3            py38h01eb140_0    conda-forge
matplotlib-base           3.5.3            py38h38b5ce0_2    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   3.0.1              pyhd8ed1ab_0    conda-forge
mock                      5.0.2              pyhd8ed1ab_0    conda-forge
mpc                       1.3.1                hfe3b2da_0    conda-forge
mpfr                      4.2.0                hb012696_0    conda-forge
mpmath                    1.3.0              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           1.0.0              pyha770c72_0    conda-forge
nbclassic                 1.0.0              pyhb4ecaf3_1    conda-forge
nbclient                  0.8.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.8.0              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.8.0              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.8.0              pyhd8ed1ab_0    conda-forge
nbformat                  5.9.2              pyhd8ed1ab_0    conda-forge
nbsphinx                  0.9.3              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  3.1                pyhd8ed1ab_0    conda-forge
nomkl                     1.0                  h5ca1d4c_0    conda-forge
notebook                  7.0.3              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.3              pyhd8ed1ab_0    conda-forge
numba                     0.53.1           py38h8b71fd7_1    conda-forge
numexpr                   2.8.3           py38h97b1c41_100    conda-forge
numpy                     1.19.5           py38h8246c76_3    conda-forge
numpydoc                  1.5.0              pyhd8ed1ab_0    conda-forge
openjpeg                  2.5.0                h488ebb8_3    conda-forge
openssl                   3.1.2                hd590300_0    conda-forge
overrides                 7.4.0              pyhd8ed1ab_0    conda-forge
packaging                 23.1               pyhd8ed1ab_0    conda-forge
pandas                    1.0.5            py38hcb8c335_0    conda-forge
pandoc                    3.1.3                h32600fe_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
pango                     1.50.14              ha41ecd1_2    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathspec                  0.11.2             pyhd8ed1ab_0    conda-forge
pbr                       5.11.1             pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pcre2                     10.40                hc3806b6_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.0.1           py38h71741d6_0    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              3.10.0             pyhd8ed1ab_0    conda-forge
plotly                    5.17.0             pyhd8ed1ab_0    conda-forge
pluggy                    1.3.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.17.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.39             pyha770c72_0    conda-forge
prompt_toolkit            3.0.39               hd8ed1ab_0    conda-forge
psutil                    5.9.5            py38h1de0b5d_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
py                        1.11.0             pyh6c4a22f_0    conda-forge
pybtex                    0.24.0             pyhd8ed1ab_2    conda-forge
pybtex-docutils           1.0.3            py38h578d9bd_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyerfa                    2.0.0.1          py38h71d37f0_2    conda-forge
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pygraphviz                1.11             py38h83a7919_0    conda-forge
pyopenssl                 23.1.1             pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.3           py38h1de0b5d_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
pytables                  3.7.0            py38hf632491_2    conda-forge
pytest                    7.4.2              pyhd8ed1ab_0    conda-forge
pytest-cov                4.1.0              pyhd8ed1ab_0    conda-forge
pytest-doctestplus        1.0.0              pyhd8ed1ab_0    conda-forge
pytest-html               3.2.0              pyhd8ed1ab_1    conda-forge
pytest-metadata           3.0.0              pyhd8ed1ab_1    conda-forge
python                    3.8.17          he550d4f_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-dokuwiki           1.3.3              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.18.0             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.8                      3_cp38    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1            py38h01eb140_0    conda-forge
pyzmq                     25.1.1           py38h509eb50_0    conda-forge
qgrid                     1.3.1              pyhd8ed1ab_4    conda-forge
radioactivedecay          0.4.21             pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
recommonmark              0.7.1              pyhd8ed1ab_0    conda-forge
referencing               0.30.2             pyhd8ed1ab_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.10.3           py38h0cc4f7c_0    conda-forge
scipy                     1.5.3            py38hb2138dd_0    conda-forge
send2trash                1.8.2              pyh41d4057_0    conda-forge
setuptools                59.8.0           py38h578d9bd_1    conda-forge
setuptools-scm            6.4.2              pyhd8ed1ab_0    conda-forge
setuptools_scm            6.4.2                hd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
snakeviz                  2.2.0              pyhd8ed1ab_0    conda-forge
snappy                    1.1.10               h9fff704_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
sphinx                    7.0.1              pyhd8ed1ab_0    conda-forge
sphinx-astropy            1.9.1              pyhd8ed1ab_0    conda-forge
sphinx-automodapi         0.16.0             pyh6ff6d48_0    conda-forge
sphinx-gallery            0.14.0             pyhd8ed1ab_0    conda-forge
sphinx-jsonschema         1.19.1             pyhd8ed1ab_0    conda-forge
sphinx_bootstrap_theme    0.8.1              pyhd8ed1ab_0    conda-forge
sphinx_rtd_theme          1.3.0              pyha770c72_0    conda-forge
sphinxcontrib-apidoc      0.3.0                      py_1    conda-forge
sphinxcontrib-applehelp   1.0.4              pyhd8ed1ab_0    conda-forge
sphinxcontrib-bibtex      2.5.0              pyhd8ed1ab_0    conda-forge
sphinxcontrib-devhelp     1.0.2                      py_0    conda-forge
sphinxcontrib-htmlhelp    2.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-jquery      4.1                pyhd8ed1ab_0    conda-forge
sphinxcontrib-jsmath      1.0.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-qthelp      1.0.3                      py_0    conda-forge
sphinxcontrib-serializinghtml 1.1.5              pyhd8ed1ab_2    conda-forge
sqlite                    3.40.0               h4ff8645_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
sympy                     1.12            pypyh9d50eac_103    conda-forge
tardis                    2023.10.4.0.dev7+g70fcf0b          pypi_0    pypi
tenacity                  8.2.3              pyhd8ed1ab_0    conda-forge
terminado                 0.17.1             pyh41d4057_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.3.3            py38h01eb140_0    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.10.0             pyhd8ed1ab_0    conda-forge
typed-ast                 1.5.5            py38h01eb140_0    conda-forge
typing-extensions         4.7.1                hd8ed1ab_0    conda-forge
typing_extensions         4.7.1              pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
unicodedata2              15.0.0           py38h0a891b7_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.0.4              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.6              pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.6.3              pyhd8ed1ab_0    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.6              pyhd8ed1ab_0    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.1.1                hd590300_0    conda-forge
xorg-libsm                1.2.4                h7391055_0    conda-forge
xorg-libx11               1.8.6                h8ee46fc_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h0b41bf4_2    conda-forge
xorg-libxrender           0.9.11               hd590300_0    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h0b41bf4_1003    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zipp                      3.16.2             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

Additional context
First time TARDIS user!

[andrewfullard]

Hi Chris. Thanks for making an issue. We are currently working to update our documentation and release process to resolve this issue. In the meantime, you can download the lockfile directly from github to use the latest version (the previous "latest release" is from before our environment update).

[atharva-2001]

@chrisfrohmaier Would you mind letting us know if this issue was resolved for you?

I believe the issue you faced is due to an outdated environment, which we recently changed, and I guess all you need to do is to update it with the latest lockfile!
conda update --name tardis --file conda-{platform}-64.lock

As Andrew said, you could get the lockfile directly from GitHub-
https://github.com/tardis-sn/tardis/blob/master/conda-osx-64.lock
https://github.com/tardis-sn/tardis/blob/master/conda-linux-64.lock

if that doesn't work, perhaps try a fresh installation?-

After creating the installation, you could do this the pip way-
pip install git+https://github.com/tardis-sn/tardis.git@master

or using tags- https://github.com/tardis-sn/tardis/tags

$ pip install git+https://github.com/tardis-sn/tardis.git@{tag}

For example-

pip install git+https://github.com/tardis-sn/tardis.git@release-2023.09.17

[chrisfrohmaier]

Hi,
I'm afraid I have a new error. I've decided to try and install only on our group's linux server and have given up on my Mac (solving conda environments takes too long)

I have created a conda environment using the new conda-linux-64.lock file, I then tried to install via:
pip install git+https://github.com/tardis-sn/tardis.git@master

I then followed the Quickstart instruction, but fail here:

In [1]: from tardis import run_tardis
Iterations:                                                                                0/? [00:00<?, ?it/s]
In [2]:
   ...: sim = run_tardis("tardis_example.yml",
   ...:                  virtual_packet_logging=True,
   ...:                  show_convergence_plots=True,
   ...:                  export_convergence_plots=True,
   ...:                  log_level="INFO")
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
Cell In[2], line 1
----> 1 sim = run_tardis("tardis_example.yml",
      2                  virtual_packet_logging=True,
      3                  show_convergence_plots=True,
      4                  export_convergence_plots=True,
      5                  log_level="INFO")

File ~/anaconda3/envs/tardis_py/lib/python3.11/site-packages/tardis/base.py:82, in run_tardis(config, atom_data, packet_source, simulation_callbacks, virtual_packet_logging, show_convergence_plots, log_level, specific_log_level, show_progress_bars, **kwargs)
     80 else:
     81     try:
---> 82         tardis_config = Configuration.from_yaml(config)
     83     except TypeError:
     84         logger.debug(
     85             "TARDIS Config not available via YAML. Reading through TARDIS Config Dictionary"
     86         )

File ~/anaconda3/envs/tardis_py/lib/python3.11/site-packages/tardis/io/configuration/config_reader.py:230, in Configuration.from_yaml(cls, fname, *args, **kwargs)
    224     raise ConfigurationError(
    225         "Currently only tardis_config_version v1.0 supported"
    226     )
    228 kwargs["config_dirname"] = os.path.dirname(fname)
--> 230 return cls.from_config_dict(yaml_dict, *args, **kwargs)

File ~/anaconda3/envs/tardis_py/lib/python3.11/site-packages/tardis/io/configuration/config_reader.py:250, in Configuration.from_config_dict(cls, config_dict, validate, config_dirname)
    234 """
    235 Validating and subsequently parsing a config file.
    236
   (...)
    246 `tardis.config_reader.Configuration`
    247 """
    249 if validate:
--> 250     validated_config_dict = config_validator.validate_dict(config_dict)
    251 else:
    252     validated_config_dict = config_dict

File ~/anaconda3/envs/tardis_py/lib/python3.11/site-packages/tardis/io/configuration/config_validator.py:90, in validate_dict(config_dict, schemapath, validator)
     85 def validate_dict(
     86     config_dict,
     87     schemapath=CONFIG_SCHEMA_FNAME,
     88     validator=DefaultDraft4Validator,
     89 ):
---> 90     with open(schemapath) as f:
     91         schema = yaml.load(f, Loader=YAMLLoader)
     92     schemaurl = f"file://{schemapath}"

FileNotFoundError: [Errno 2] No such file or directory: '/home/cgtp1g20/anaconda3/envs/tardis_py/lib/python3.11/site-packages/tardis/io/configuration/schemas/base.yml'

When I investigate the directory, I can only get as far as/home/cgtp1g20/anaconda3/envs/tardis_py/lib/python3.11/site-packages/tardis/io/configuration/ subsequent directories were not created. Does this mean the setup.py file needs to be modified so that all directories in the GitHub repo are copied over?

[atharva-2001]

Hi @chrisfrohmaier, thank you for letting us know this. This was really helpful and I was able to reproduce the issue. Until this is fixed completely, would you mind trying this out? This is the developer way and should work for the time being.

Please let me know if you face issues. I'd recommend you to delete the anaconda3 tardis folder to make sure the tardis installed here doesn't mess with that.

Once you've installed the env using the lock file-

$ git clone git@github.com:tardis-sn/tardis.git
$ cd tardis
$ git remote add upstream git@github.com:tardis-sn/tardis.git
$ git fetch upstream
$ git checkout upstream/master
$ python setup.py develop

[atharva-2001]

Hi @chrisfrohmaier Would you mind letting us know if this issue was resolved?

[chrisfrohmaier]

Hello @atharva-2001 Yes, this was resolved and were are able to use Tardis. Thanks for your help!

[atharva-2001]

Awesome! If you run into other errors, please feel free to open another issue or comment on this one. Thank you for creating this issue!!