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mmcguffi / pLannotate

Webserver and command line tool for annotating engineered plasmids
GNU General Public License v3.0
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`st.cache` is deprecated #39

Closed bcantarel closed 5 months ago

bcantarel commented 5 months ago
: MADV_DONTNEED does not work (memset will be used instead) : (This is the expected behaviour if you are running under QEMU) 2024-01-28 22:23:41.053 Warning: to view this Streamlit app on a browser, run it with the following command: streamlit run /opt/conda/bin/plannotate [ARGUMENTS] 2024-01-28 22:24:20.154 `st.cache` is deprecated. Please use one of Streamlit's new caching commands, `st.cache_data` or `st.cache_resource`. More information [in our docs](https://docs.streamlit.io/library/advanced-features/caching). Traceback (most recent call last): File "/opt/conda/bin/plannotate", line 33, in sys.exit(load_entry_point('plannotate==1.2.1', 'console_scripts', 'plannotate')()) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.11/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.11/site-packages/plannotate/pLannotate.py", line 116, in main_batch recordDf = annotate(inSeq, yaml_file, linear, detailed) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.11/site-packages/plannotate/annotate.py", line 355, in annotate blastDf = clean(blastDf) ^^^^^^^^^^^^^^ File "/opt/conda/lib/python3.11/site-packages/plannotate/annotate.py", line 178, in clean rowSlice = (seqSpace[columnSlice] == kind).any(1) #only the rows that are in the columns of hit ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: DataFrame.any() takes 1 positional argument but 2 were given
mmcguffi commented 5 months ago

Hi @bcantarel I need more information to help you. How did you install pLannotate? What platform are you on? What commands did you use?

bcantarel commented 5 months ago

I used mamba like on the Readme: mamba install plannotate

mmcguffi commented 5 months ago

Hi @bcantarel -- I was not able to replicate your issues manually, nor via automated tests: https://github.com/mmcguffi/pLannotate/actions

My best guess is that you are trying to install into an existing conda environment that already has conflicting tools -- I cannot guarantee that plannotate will work in these situations since I cannot test them. I suggest a fresh install as outlined in the readme:

mamba create -n plannotate -c conda-forge -c bioconda plannotate