Issues with installing 1.4

[IHaydon]

Hi all,

I had to re-install FESTIM on my machine last week, and I’m running into some issues. Installing the latest version has installed version 2.0a3 (from print(F.__version__)), but now when I attempt to run through the workshop task 1 to check it all, I’m running into this:

my_model = F.Simulation()

---

AttributeError Traceback (most recent call last)
Cell In[2], line 1
----> 1 my_model = F.Simulation()

AttributeError: module ‘festim’ has no attribute ‘Simulation’

I was running under the assumption this might be a version issue, so I’m trying to get 1.4 installed, but I’m facing more errors:

conda uninstall festim

PackagesNotFoundError: The following packages are missing from the target environment:
- festim 

and then also this:

conda install -c conda-forge festim==1.4 

Retrieving notices: ...working... done
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: | Killed

Help?

[VVKulagin]

Hi @IHaydon!

I had to re-install FESTIM on my machine last week, and I’m running into some issues. Installing the latest version has installed version 2.0a3 (from print(F.__version__) ), but now when I attempt to run through the workshop task 1 to check it all, I’m running into this:

FESTIM 2.0a3 indeed does not have the Simulation class. For this alpha-version, you might want to check the corresponding API reference page of the documentation. Moreover, the Workshop is being updated to follow the new version. In general, you can choose an appropriate version of docs/workshop in the Read the Docs menu usually located in the lower right corner.

Screenshot

I was running under the assumption this might be a version issue, so I’m trying to get 1.4 installed, but I’m facing more errors:

Maybe, you should try the following command to remove the package:

conda remove festim

Though both commands worked on my side.

Meanwhile, I managed to sucessfully install FESTIM 1.4 from scratch following the FESTIM installation instructions. Would you mind showing the list of installed dependecies with conda list and the conda version conda -V?

[IHaydon]

Hiya!

Conda is still saying FESTIM doesn’t exist, even though I can run the code to get the version, no change between the uninstall and the remove commands. I’m very confused how conda can’t find a festim package, but I can run some things?

As requested, here are the following:

(base) XXXX:~/FESTIM-workshop$ conda list
# packages in environment at /home/gy3715/anaconda3:
#
# Name                    Version                   Build  Channel
_anaconda_depends         2024.10             py312_mkl_0  
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
aiobotocore               2.12.3          py312h06a4308_0  
aiohappyeyeballs          2.4.0           py312h06a4308_0  
aiohttp                   3.10.5          py312h5eee18b_0  
aioitertools              0.7.1              pyhd3eb1b0_0  
aiosignal                 1.2.0              pyhd3eb1b0_0  
alabaster                 0.7.16          py312h06a4308_0  
altair                    5.0.1           py312h06a4308_0  
anaconda-anon-usage       0.4.4           py312hfc0e8ea_100  
anaconda-catalogs         0.2.0           py312h06a4308_1  
anaconda-client           1.12.3          py312h06a4308_0  
anaconda-cloud-auth       0.5.1           py312h06a4308_0  
anaconda-navigator        2.6.3           py312h06a4308_0  
anaconda-project          0.11.1          py312h06a4308_0  
annotated-types           0.6.0           py312h06a4308_0  
anyio                     4.2.0           py312h06a4308_0  
aom                       3.6.0                h6a678d5_0  
appdirs                   1.4.4              pyhd3eb1b0_0  
archspec                  0.2.3              pyhd3eb1b0_0  
argon2-cffi               21.3.0             pyhd3eb1b0_0  
argon2-cffi-bindings      21.2.0          py312h5eee18b_0  
arrow                     1.2.3           py312h06a4308_1  
arrow-cpp                 16.1.0               hc1eb8f0_0  
astroid                   2.14.2          py312h06a4308_0  
astropy                   6.1.3           py312h5eee18b_0  
astropy-iers-data         0.2024.9.2.0.33.23 py312h06a4308_0  
asttokens                 2.0.5              pyhd3eb1b0_0  
async-lru                 2.0.4           py312h06a4308_0  
atomicwrites              1.4.0                      py_0  
attrs                     23.1.0          py312h06a4308_0  
automat                   20.2.0                     py_0  
autopep8                  2.0.4              pyhd3eb1b0_0  
aws-c-auth                0.6.19               h5eee18b_0  
aws-c-cal                 0.5.20               hdbd6064_0  
aws-c-common              0.8.5                h5eee18b_0  
aws-c-compression         0.2.16               h5eee18b_0  
aws-c-event-stream        0.2.15               h6a678d5_0  
aws-c-http                0.6.25               h5eee18b_0  
aws-c-io                  0.13.10              h5eee18b_0  
aws-c-mqtt                0.7.13               h5eee18b_0  
aws-c-s3                  0.1.51               hdbd6064_0  
aws-c-sdkutils            0.1.6                h5eee18b_0  
aws-checksums             0.1.13               h5eee18b_0  
aws-crt-cpp               0.18.16              h6a678d5_0  
aws-sdk-cpp               1.10.55              h721c034_0  
babel                     2.11.0          py312h06a4308_0  
bcrypt                    3.2.0           py312h5eee18b_1  
beautifulsoup4            4.12.3          py312h06a4308_0  
binaryornot               0.4.4              pyhd3eb1b0_1  
black                     24.8.0          py312h06a4308_0  
blas                      1.0                         mkl  
bleach                    4.1.0              pyhd3eb1b0_0  
blinker                   1.6.2           py312h06a4308_0  
blosc                     1.21.3               h6a678d5_0  
bokeh                     3.6.0           py312h06a4308_0  
boltons                   23.0.0          py312h06a4308_0  
boost-cpp                 1.82.0               hdb19cb5_2  
botocore                  1.34.69         py312h06a4308_0  
bottleneck                1.3.7           py312ha883a20_0  
brotli                    1.0.9                h5eee18b_8  
brotli-bin                1.0.9                h5eee18b_8  
brotli-python             1.0.9           py312h6a678d5_8  
brunsli                   0.1                  h2531618_0  
bzip2                     1.0.8                h5eee18b_6  
c-ares                    1.19.1               h5eee18b_0  
c-blosc2                  2.12.0               h80c7b02_0  
ca-certificates           2024.9.24            h06a4308_0  
cachetools                5.3.3           py312h06a4308_0  
certifi                   2024.8.30       py312h06a4308_0  
cffi                      1.17.1          py312h1fdaa30_0  
cfitsio                   3.470                h5893167_7  
chardet                   4.0.0           py312h06a4308_1003  
charls                    2.2.0                h2531618_0  
charset-normalizer        3.3.2              pyhd3eb1b0_0  
click                     8.1.7           py312h06a4308_0  
cloudpickle               3.0.0           py312h06a4308_0  
colorama                  0.4.6           py312h06a4308_0  
colorcet                  3.1.0           py312h06a4308_0  
comm                      0.2.1           py312h06a4308_0  
conda                     24.9.2          py312h06a4308_0  
conda-build               24.9.0          py312h06a4308_0  
conda-content-trust       0.2.0           py312h06a4308_1  
conda-index               0.5.0           py312h06a4308_0  
conda-libmamba-solver     24.9.0             pyhd3eb1b0_0  
conda-pack                0.7.1           py312h06a4308_0  
conda-package-handling    2.3.0           py312h06a4308_0  
conda-package-streaming   0.10.0          py312h06a4308_0  
conda-repo-cli            1.0.114         py312h06a4308_0  
conda-token               0.5.0              pyhd3eb1b0_0  
constantly                23.10.4         py312h06a4308_0  
contourpy                 1.2.0           py312hdb19cb5_0  
cookiecutter              2.6.0           py312h06a4308_0  
cryptography              43.0.0          py312hdda0065_0  
cssselect                 1.2.0           py312h06a4308_0  
curl                      8.9.1                hdbd6064_0  
cycler                    0.11.0             pyhd3eb1b0_0  
cyrus-sasl                2.1.28               h52b45da_1  
cytoolz                   0.12.2          py312h5eee18b_0  
dask                      2024.8.2        py312h06a4308_0  
dask-core                 2024.8.2        py312h06a4308_0  
dask-expr                 1.1.13          py312h06a4308_0  
datashader                0.16.3          py312h06a4308_0  
dav1d                     1.2.1                h5eee18b_0  
dbus                      1.13.18              hb2f20db_0  
debugpy                   1.6.7           py312h6a678d5_0  
decorator                 5.1.1              pyhd3eb1b0_0  
defusedxml                0.7.1              pyhd3eb1b0_0  
diff-match-patch          20200713           pyhd3eb1b0_0  
dill                      0.3.8           py312h06a4308_0  
distributed               2024.8.2        py312h06a4308_0  
distro                    1.9.0           py312h06a4308_0  
docstring-to-markdown     0.11            py312h06a4308_0  
docutils                  0.18.1          py312h06a4308_3  
et_xmlfile                1.1.0           py312h06a4308_1  
executing                 0.8.3              pyhd3eb1b0_0  
expat                     2.6.3                h6a678d5_0  
filelock                  3.13.1          py312h06a4308_0  
flake8                    7.0.0           py312h06a4308_0  
flask                     3.0.3           py312h06a4308_0  
fmt                       9.1.0                hdb19cb5_1  
fontconfig                2.14.1               h4c34cd2_2  
fonttools                 4.51.0          py312h5eee18b_0  
freetype                  2.12.1               h4a9f257_0  
frozendict                2.4.2           py312h06a4308_0  
frozenlist                1.4.0           py312h5eee18b_0  
fsspec                    2024.6.1        py312h06a4308_0  
gensim                    4.3.3           py312h526ad5a_0  
gflags                    2.2.2                h6a678d5_1  
giflib                    5.2.1                h5eee18b_3  
gitdb                     4.0.7              pyhd3eb1b0_0  
gitpython                 3.1.43          py312h06a4308_0  
glib                      2.78.4               h6a678d5_0  
glib-tools                2.78.4               h6a678d5_0  
glog                      0.5.0                h6a678d5_1  
greenlet                  3.0.1           py312h6a678d5_0  
gst-plugins-base          1.14.1               h6a678d5_1  
gstreamer                 1.14.1               h5eee18b_1  
h11                       0.14.0          py312h06a4308_0  
h5py                      3.11.0          py312h34c39bb_0  
hdf5                      1.12.1               h2b7332f_3  
heapdict                  1.0.1              pyhd3eb1b0_0  
holoviews                 1.19.1          py312h06a4308_0  
httpcore                  1.0.2           py312h06a4308_0  
httpx                     0.27.0          py312h06a4308_0  
hvplot                    0.11.0          py312h06a4308_0  
hyperlink                 21.0.0             pyhd3eb1b0_0  
icu                       73.1                 h6a678d5_0  
idna                      3.7             py312h06a4308_0  
imagecodecs               2023.1.23       py312h81b8100_1  
imageio                   2.33.1          py312h06a4308_0  
imagesize                 1.4.1           py312h06a4308_0  
imbalanced-learn          0.12.3          py312h06a4308_1  
importlib-metadata        7.0.1           py312h06a4308_0  
incremental               22.10.0            pyhd3eb1b0_0  
inflection                0.5.1           py312h06a4308_1  
iniconfig                 1.1.1              pyhd3eb1b0_0  
intake                    2.0.7           py312h06a4308_0  
intel-openmp              2023.1.0         hdb19cb5_46306  
intervaltree              3.1.0              pyhd3eb1b0_0  
ipykernel                 6.28.0          py312h06a4308_0  
ipython                   8.27.0          py312h06a4308_0  
ipython_genutils          0.2.0              pyhd3eb1b0_1  
ipywidgets                7.8.1           py312h06a4308_0  
isort                     5.13.2          py312h06a4308_0  
itemadapter               0.3.0              pyhd3eb1b0_0  
itemloaders               1.1.0           py312h06a4308_0  
itsdangerous              2.2.0           py312h06a4308_0  
jaraco.classes            3.2.1              pyhd3eb1b0_0  
jedi                      0.19.1          py312h06a4308_0  
jeepney                   0.7.1              pyhd3eb1b0_0  
jellyfish                 1.0.1           py312hb02cf49_0  
jinja2                    3.1.4           py312h06a4308_0  
jmespath                  1.0.1           py312h06a4308_0  
joblib                    1.4.2           py312h06a4308_0  
jpeg                      9e                   h5eee18b_3  
jq                        1.6               h27cfd23_1000  
json5                     0.9.6              pyhd3eb1b0_0  
jsonpatch                 1.33            py312h06a4308_1  
jsonpointer               2.1                pyhd3eb1b0_0  
jsonschema                4.23.0          py312h06a4308_0  
jsonschema-specifications 2023.7.1        py312h06a4308_0  
jupyter                   1.0.0           py312h06a4308_9  
jupyter-lsp               2.2.0           py312h06a4308_0  
jupyter_client            8.6.0           py312h06a4308_0  
jupyter_console           6.6.3           py312h06a4308_1  
jupyter_core              5.7.2           py312h06a4308_0  
jupyter_events            0.10.0          py312h06a4308_0  
jupyter_server            2.14.1          py312h06a4308_0  
jupyter_server_terminals  0.4.4           py312h06a4308_1  
jupyterlab                4.2.5           py312h06a4308_0  
jupyterlab-variableinspector 3.1.0           py312h06a4308_0  
jupyterlab_pygments       0.1.2                      py_0  
jupyterlab_server         2.27.3          py312h06a4308_0  
jupyterlab_widgets        1.0.0              pyhd3eb1b0_1  
jxrlib                    1.1                  h7b6447c_2  
keyring                   24.3.1          py312h06a4308_0  
kiwisolver                1.4.4           py312h6a678d5_0  
krb5                      1.20.1               h143b758_1  
lazy-object-proxy         1.10.0          py312h5eee18b_0  
lazy_loader               0.4             py312h06a4308_0  
lcms2                     2.12                 h3be6417_0  
ld_impl_linux-64          2.40                 h12ee557_0  
lerc                      3.0                  h295c915_0  
libabseil                 20240116.2      cxx17_h6a678d5_0  
libaec                    1.0.4                he6710b0_1  
libarchive                3.6.2                h6ac8c49_3  
libavif                   0.11.1               h5eee18b_0  
libboost                  1.82.0               h109eef0_2  
libbrotlicommon           1.0.9                h5eee18b_8  
libbrotlidec              1.0.9                h5eee18b_8  
libbrotlienc              1.0.9                h5eee18b_8  
libclang                  14.0.6          default_hc6dbbc7_1  
libclang13                14.0.6          default_he11475f_1  
libcups                   2.4.2                h2d74bed_1  
libcurl                   8.9.1                h251f7ec_0  
libdeflate                1.17                 h5eee18b_1  
libedit                   3.1.20230828         h5eee18b_0  
libev                     4.33                 h7f8727e_1  
libevent                  2.1.12               hdbd6064_1  
libffi                    3.4.4                h6a678d5_1  
libgcc-ng                 11.2.0               h1234567_1  
libgfortran-ng            11.2.0               h00389a5_1  
libgfortran5              11.2.0               h1234567_1  
libglib                   2.78.4               hdc74915_0  
libgomp                   11.2.0               h1234567_1  
libgrpc                   1.62.2               h2d74bed_0  
libiconv                  1.16                 h5eee18b_3  
liblief                   0.12.3               h6a678d5_0  
libllvm14                 14.0.6               hecde1de_4  
libmamba                  1.5.8                hfe524e5_2  
libmambapy                1.5.8           py312h2dafd23_2  
libnghttp2                1.57.0               h2d74bed_0  
libpng                    1.6.39               h5eee18b_0  
libpq                     12.17                hdbd6064_0  
libprotobuf               4.25.3               he621ea3_0  
libsodium                 1.0.18               h7b6447c_0  
libsolv                   0.7.24               he621ea3_1  
libspatialindex           1.9.3                h2531618_0  
libssh2                   1.11.0               h251f7ec_0  
libstdcxx-ng              11.2.0               h1234567_1  
libthrift                 0.15.0               h1795dd8_2  
libtiff                   4.5.1                h6a678d5_0  
libuuid                   1.41.5               h5eee18b_0  
libwebp-base              1.3.2                h5eee18b_0  
libxcb                    1.15                 h7f8727e_0  
libxkbcommon              1.0.1                h5eee18b_1  
libxml2                   2.10.4               hfdd30dd_2  
libxslt                   1.1.37               h5eee18b_1  
libzopfli                 1.0.3                he6710b0_0  
linkify-it-py             2.0.0           py312h06a4308_0  
llvmlite                  0.43.0          py312h6a678d5_0  
locket                    1.0.0           py312h06a4308_0  
lxml                      5.2.1           py312hdbbb534_0  
lz4                       4.3.2           py312h5eee18b_0  
lz4-c                     1.9.4                h6a678d5_1  
lzo                       2.10                 h7b6447c_2  
markdown                  3.4.1           py312h06a4308_0  
markdown-it-py            2.2.0           py312h06a4308_1  
markupsafe                2.1.3           py312h5eee18b_0  
matplotlib                3.9.2           py312h06a4308_0  
matplotlib-base           3.9.2           py312h66fe004_0  
matplotlib-inline         0.1.6           py312h06a4308_0  
mccabe                    0.7.0              pyhd3eb1b0_0  
mdit-py-plugins           0.3.0           py312h06a4308_0  
mdurl                     0.1.0           py312h06a4308_0  
menuinst                  2.1.2           py312h06a4308_0  
mistune                   2.0.4           py312h06a4308_0  
mkl                       2023.1.0         h213fc3f_46344  
mkl-service               2.4.0           py312h5eee18b_1  
mkl_fft                   1.3.10          py312h5eee18b_0  
mkl_random                1.2.7           py312h526ad5a_0  
more-itertools            10.3.0          py312h06a4308_0  
mpmath                    1.3.0           py312h06a4308_0  
msgpack-python            1.0.3           py312hdb19cb5_0  
multidict                 6.0.4           py312h5eee18b_0  
multipledispatch          0.6.0           py312h06a4308_0  
mypy                      1.11.2          py312h5eee18b_0  
mypy_extensions           1.0.0           py312h06a4308_0  
mysql                     5.7.24               h721c034_2  
navigator-updater         0.5.1           py312h06a4308_0  
nbclient                  0.8.0           py312h06a4308_0  
nbconvert                 7.16.4          py312h06a4308_0  
nbformat                  5.10.4          py312h06a4308_0  
ncurses                   6.4                  h6a678d5_0  
nest-asyncio              1.6.0           py312h06a4308_0  
networkx                  3.3             py312h06a4308_0  
nltk                      3.9.1           py312h06a4308_0  
notebook                  7.2.2           py312h06a4308_1  
notebook-shim             0.2.3           py312h06a4308_0  
nspr                      4.35                 h6a678d5_0  
nss                       3.89.1               h6a678d5_0  
numba                     0.60.0          py312h526ad5a_0  
numexpr                   2.8.7           py312hf827012_0  
numpy                     1.26.4          py312hc5e2394_0  
numpy-base                1.26.4          py312h0da6c21_0  
numpydoc                  1.7.0           py312h06a4308_0  
oniguruma                 6.9.7.1              h27cfd23_0  
openjpeg                  2.5.2                he7f1fd0_0  
openpyxl                  3.1.5           py312h5eee18b_0  
openssl                   3.0.15               h5eee18b_0  
orc                       2.0.1                h2d29ad5_0  
overrides                 7.4.0           py312h06a4308_0  
packaging                 24.1            py312h06a4308_0  
pandas                    2.2.2           py312h526ad5a_0  
pandocfilters             1.5.0              pyhd3eb1b0_0  
panel                     1.5.2           py312h06a4308_0  
param                     2.1.1           py312h06a4308_0  
parsel                    1.8.1           py312h06a4308_0  
parso                     0.8.3              pyhd3eb1b0_0  
partd                     1.4.1           py312h06a4308_0  
patch                     2.7.6             h7b6447c_1001  
patchelf                  0.17.2               h6a678d5_0  
pathspec                  0.10.3          py312h06a4308_0  
patsy                     0.5.6           py312h06a4308_0  
pcre2                     10.42                hebb0a14_1  
pexpect                   4.8.0              pyhd3eb1b0_3  
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    10.4.0          py312h5eee18b_0  
pip                       24.2            py312h06a4308_0  
pkce                      1.0.3           py312h06a4308_0  
pkginfo                   1.10.0          py312h06a4308_0  
platformdirs              3.10.0          py312h06a4308_0  
plotly                    5.24.1          py312he106c6f_0  
pluggy                    1.0.0           py312h06a4308_1  
ply                       3.11            py312h06a4308_1  
prometheus_client         0.14.1          py312h06a4308_0  
prompt-toolkit            3.0.43          py312h06a4308_0  
prompt_toolkit            3.0.43               hd3eb1b0_0  
protego                   0.1.16                     py_0  
protobuf                  4.25.3          py312h12ddb61_0  
psutil                    5.9.0           py312h5eee18b_0  
ptyprocess                0.7.0              pyhd3eb1b0_2  
pure_eval                 0.2.2              pyhd3eb1b0_0  
py-cpuinfo                9.0.0           py312h06a4308_0  
py-lief                   0.12.3          py312h6a678d5_0  
pyarrow                   16.1.0          py312h526ad5a_0  
pyasn1                    0.4.8              pyhd3eb1b0_0  
pyasn1-modules            0.2.8                      py_0  
pybind11-abi              5                    hd3eb1b0_0  
pycodestyle               2.11.1          py312h06a4308_0  
pycosat                   0.6.6           py312h5eee18b_1  
pycparser                 2.21               pyhd3eb1b0_0  
pyct                      0.5.0           py312h06a4308_0  
pycurl                    7.45.3          py312hdbd6064_0  
pydantic                  2.8.2           py312h06a4308_0  
pydantic-core             2.20.1          py312hb02cf49_0  
pydeck                    0.8.0           py312h06a4308_2  
pydispatcher              2.0.5           py312h06a4308_3  
pydocstyle                6.3.0           py312h06a4308_0  
pyerfa                    2.0.1.4         py312ha883a20_0  
pyflakes                  3.2.0           py312h06a4308_0  
pygments                  2.15.1          py312h06a4308_1  
pyjwt                     2.8.0           py312h06a4308_0  
pylint                    2.16.2          py312h06a4308_0  
pylint-venv               3.0.3           py312h06a4308_0  
pyls-spyder               0.4.0              pyhd3eb1b0_0  
pyodbc                    5.1.0           py312h6a678d5_0  
pyopenssl                 24.2.1          py312h06a4308_0  
pyparsing                 3.1.2           py312h06a4308_0  
pyqt                      5.15.10         py312h6a678d5_0  
pyqt5-sip                 12.13.0         py312h5eee18b_0  
pyqtwebengine             5.15.10         py312h6a678d5_0  
pysocks                   1.7.1           py312h06a4308_0  
pytables                  3.10.1          py312h387d6ec_0  
pytest                    7.4.4           py312h06a4308_0  
python                    3.12.7               h5148396_0  
python-dateutil           2.9.0post0      py312h06a4308_2  
python-dotenv             0.21.0          py312h06a4308_0  
python-fastjsonschema     2.16.2          py312h06a4308_0  
python-json-logger        2.0.7           py312h06a4308_0  
python-libarchive-c       5.1                pyhd3eb1b0_0  
python-lmdb               1.4.1           py312h6a678d5_0  
python-lsp-black          2.0.0           py312h06a4308_0  
python-lsp-jsonrpc        1.1.2              pyhd3eb1b0_0  
python-lsp-server         1.10.0          py312h06a4308_0  
python-slugify            5.0.2              pyhd3eb1b0_0  
python-tzdata             2023.3             pyhd3eb1b0_0  
pytoolconfig              1.2.6           py312h06a4308_0  
pytz                      2024.1          py312h06a4308_0  
pyviz_comms               3.0.2           py312h06a4308_0  
pywavelets                1.7.0           py312h5eee18b_0  
pyxdg                     0.27               pyhd3eb1b0_0  
pyyaml                    6.0.1           py312h5eee18b_0  
pyzmq                     25.1.2          py312h6a678d5_0  
qdarkstyle                3.2.3              pyhd3eb1b0_0  
qstylizer                 0.2.2           py312h06a4308_0  
qt-main                   5.15.2              h53bd1ea_10  
qt-webengine              5.15.9               h9ab4d14_7  
qtawesome                 1.3.1           py312h06a4308_0  
qtconsole                 5.5.1           py312h06a4308_0  
qtpy                      2.4.1           py312h06a4308_0  
queuelib                  1.6.2           py312h06a4308_0  
re2                       2022.04.01           h295c915_0  
readline                  8.2                  h5eee18b_0  
referencing               0.30.2          py312h06a4308_0  
regex                     2024.9.11       py312h5eee18b_0  
reproc                    14.2.4               h6a678d5_2  
reproc-cpp                14.2.4               h6a678d5_2  
requests                  2.32.3          py312h06a4308_0  
requests-file             1.5.1              pyhd3eb1b0_0  
requests-toolbelt         1.0.0           py312h06a4308_0  
rfc3339-validator         0.1.4           py312h06a4308_0  
rfc3986-validator         0.1.1           py312h06a4308_0  
rich                      13.7.1          py312h06a4308_0  
rope                      1.12.0          py312h06a4308_0  
rpds-py                   0.10.6          py312hb02cf49_0  
rtree                     1.0.1           py312h06a4308_0  
ruamel.yaml               0.18.6          py312h5eee18b_0  
ruamel.yaml.clib          0.2.8           py312h5eee18b_0  
ruamel_yaml               0.17.21         py312h5eee18b_0  
s2n                       1.3.27               hdbd6064_0  
s3fs                      2024.6.1        py312h06a4308_0  
scikit-image              0.24.0          py312h526ad5a_0  
scikit-learn              1.5.1           py312h526ad5a_0  
scipy                     1.13.1          py312hc5e2394_0  
scrapy                    2.11.1          py312h06a4308_0  
seaborn                   0.13.2          py312h06a4308_0  
secretstorage             3.3.1           py312h06a4308_1  
semver                    3.0.2           py312h06a4308_0  
send2trash                1.8.2           py312h06a4308_0  
service_identity          18.1.0             pyhd3eb1b0_1  
setuptools                75.1.0          py312h06a4308_0  
sip                       6.7.12          py312h6a678d5_0  
six                       1.16.0             pyhd3eb1b0_1  
smart_open                5.2.1           py312h06a4308_0  
smmap                     4.0.0              pyhd3eb1b0_0  
snappy                    1.2.1                h6a678d5_0  
sniffio                   1.3.0           py312h06a4308_0  
snowballstemmer           2.2.0              pyhd3eb1b0_0  
sortedcontainers          2.4.0              pyhd3eb1b0_0  
soupsieve                 2.5             py312h06a4308_0  
sphinx                    7.3.7           py312h5eee18b_0  
sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0  
sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0  
sphinxcontrib-htmlhelp    2.0.0              pyhd3eb1b0_0  
sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0  
sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0  
sphinxcontrib-serializinghtml 1.1.10          py312h06a4308_0  
spyder                    5.5.1           py312h06a4308_4  
spyder-kernels            2.5.0           py312h06a4308_0  
sqlalchemy                2.0.34          py312h00e1ef3_0  
sqlite                    3.45.3               h5eee18b_0  
stack_data                0.2.0              pyhd3eb1b0_0  
statsmodels               0.14.2          py312ha883a20_0  
streamlit                 1.37.1          py312h06a4308_0  
sympy                     1.13.2          py312h06a4308_0  
tabulate                  0.9.0           py312h06a4308_0  
tbb                       2021.8.0             hdb19cb5_0  
tblib                     1.7.0              pyhd3eb1b0_0  
tenacity                  8.2.3           py312h06a4308_0  
terminado                 0.17.1          py312h06a4308_0  
text-unidecode            1.3                pyhd3eb1b0_0  
textdistance              4.2.1              pyhd3eb1b0_0  
threadpoolctl             3.5.0           py312he106c6f_0  
three-merge               0.1.1              pyhd3eb1b0_0  
tifffile                  2023.4.12       py312h06a4308_0  
tinycss2                  1.2.1           py312h06a4308_0  
tk                        8.6.14               h39e8969_0  
tldextract                5.1.2           py312h06a4308_0  
toml                      0.10.2             pyhd3eb1b0_0  
tomli                     2.0.1           py312h06a4308_1  
tomlkit                   0.11.1          py312h06a4308_0  
toolz                     0.12.0          py312h06a4308_0  
tornado                   6.4.1           py312h5eee18b_0  
tqdm                      4.66.5          py312he106c6f_0  
traitlets                 5.14.3          py312h06a4308_0  
truststore                0.8.0           py312h06a4308_0  
twisted                   23.10.0         py312h06a4308_0  
typing-extensions         4.11.0          py312h06a4308_0  
typing_extensions         4.11.0          py312h06a4308_0  
tzdata                    2024b                h04d1e81_0  
uc-micro-py               1.0.1           py312h06a4308_0  
ujson                     5.10.0          py312h6a678d5_0  
unicodedata2              15.1.0          py312h5eee18b_0  
unidecode                 1.3.8           py312h06a4308_0  
unixodbc                  2.3.11               h5eee18b_0  
urllib3                   2.2.3           py312h06a4308_0  
utf8proc                  2.6.1                h5eee18b_1  
w3lib                     1.21.0             pyhd3eb1b0_0  
watchdog                  4.0.1           py312h06a4308_0  
wcwidth                   0.2.5              pyhd3eb1b0_0  
webencodings              0.5.1           py312h06a4308_2  
websocket-client          1.8.0           py312h06a4308_0  
werkzeug                  3.0.3           py312h06a4308_0  
whatthepatch              1.0.2           py312h06a4308_0  
wheel                     0.44.0          py312h06a4308_0  
widgetsnbextension        3.6.6           py312h06a4308_0  
wrapt                     1.14.1          py312h5eee18b_0  
wurlitzer                 3.0.2           py312h06a4308_0  
xarray                    2023.6.0        py312h06a4308_0  
xyzservices               2022.9.0        py312h06a4308_1  
xz                        5.4.6                h5eee18b_1  
yaml                      0.2.5                h7b6447c_0  
yaml-cpp                  0.8.0                h6a678d5_1  
yapf                      0.40.2          py312h06a4308_0  
yarl                      1.11.0          py312h5eee18b_0  
zeromq                    4.3.5                h6a678d5_0  
zfp                       1.0.0                h6a678d5_0  
zict                      3.0.0           py312h06a4308_0  
zipp                      3.17.0          py312h06a4308_0  
zlib                      1.2.13               h5eee18b_1  
zlib-ng                   2.0.7                h5eee18b_0  
zope                      1.0             py312h06a4308_1  
zope.interface            5.4.0           py312h5eee18b_0  
zstandard                 0.23.0          py312h2c38b39_0  
zstd                      1.5.6                hc292b87_0  

and

(base) XXXX:~/FESTIM-workshop$ conda -V
conda 24.9.2

Anaconda also was re-installed last week, as well as Ubuntu, as I was having issues with WSL, but I’ve followed all the installation guides as I did before, and this is my current sticking point. Still learning FESTIM myself, and all of my notes are not for FESTIM 2, so I’d rather not have to start from scratch already

[VVKulagin]

I see. Indeed, there is no FESTIM in the conda list

@IHaydon

Conda is still saying FESTIM doesn’t exist, even though I can run the code to get the version, no change between the uninstall and the remove commands. I’m very confused how conda can’t find a festim package, but I can run some things?

There might be an issue with paths or could it be that the working FESTIM version was installed via pip?

By the way, do you use a separate environment for FESTIM? From this line:

(base) XXXX:~/FESTIM-workshop$ conda list

I see that you are using the base environment

[remidm]

Hi @IHaydon and welcome to the FESTIM discourse!

I sense a conflict of different python versions here.

Let’s try and take things from the start:

1. Create a new conda environment

Deactivate the current env just in case:

conda deactivate

You should see in your terminal (base) meaning you are in your base environment

Uninstall festim just in case

conda uninstall festim

Note: you should not install packages in your base environment, it’s not recommended

2. Create a new clean environment

conda create -n my_new_env

3. Activate the new environment

conda activate my_new_env

At this stage, in your terminal you should see (my_new_env)

4. Install festim

conda install -c conda-forge "festim=1.4"

5. Check festim version

python

Then inside the python interpreter run

import festim
print(festim.__version__)

[IHaydon]

Right, did the newbie error of not getting out of the base environment when I had previously made the recommended one from the installation guide:

conda create -n festim-env 
conda activate festim-env

First line didn’t need re-running, as the environment did exist, just had to run the second.
Now that I’m in the right environment, the install of 1.4 is complete:

import festim as F

print(F.__version__)

1.4
/home/XXXX/anaconda3/envs/festim-env/lib/python3.13/site-packages/dolfin/jit/jit.py:121: RuntimeWarning: mpi4py.MPI.Session size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
def compile_class(cpp_data, mpi_comm=MPI.comm_world):

I’m hoping and assuming this extra message is just an artefact of my struggles, and won’t be an issue? Going through Task 1 again has also brought this similar message here:

my_model.initialise()

my_model.run()

Calling FFC just-in-time (JIT) compiler, this may take some time.
/home/XXXX/anaconda3/envs/festim-env/lib/python3.13/site-packages/dolfin/jit/jit.py:46: RuntimeWarning: mpi4py.MPI.Session size changed, may indicate binary incompatibility. Expected 32 from C header, got 40 from PyObject
if MPI.size(mpi_comm) == 1:

And further down I’m getting an error that it doesn’t have matplotlib as a module:

ModuleNotFoundError: No module named ‘matplotlib’

Running (festim-env) XXXX:~/FESTIM-workshop$ conda install conda-forge::matplotlib has now worked though, so that’s all sorted now.

Thanks for the help, hopefully I won’t be back for more too soon!

[remidm]

Don’t worry, we like “newbie erros” because they are easier to solve than core bugs

regarding this MPI warning, i can’t say I’ve already seen it. But you may want to delete this environment and start fresh and see if that solves it.

[remidm]

Also

• Did you notice the workshop has now been converted to a website?
• For running all the tasks, you will need additional dependencies (eg. matplotlib, scipy, etc.). You can install them all using this environment file in the workshop repository then run:

conda env create -f environment.yml