Updating requirements.txt and removing NP checkpointing #121
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…er recent implementations of Plotly/dataframe interactivity by Streamlit team. Also update the logo figure height from 150 to 250 since the recent st.logo() implementation in Streamlit affects that setting
…longer works, probably just need to force a key update for the selection like I do for the just-added reset button
…plot chart key; now the reset button works as expected, but the chart still resets its zoom if anything such as selection or slider changing etc. modifies the selected region. If I pursue this as users probably want, it would require the original idea of toggling the plotly box selection between a zoom, i.e. manually setting it, and the actual histogram region selection functionality which is already implemented
…ion of positive region of the histogram(s) or the x axis zoom
…lumn for filtering is changed
…PU when Squidpy is selected since it commandeers threads; in future we'll need to limit just the significance calculations to a single thread if Squidpy is selected
…aframes in Streamlit, to replace previous image filters such as in the multiaxial gater and probably in the plotter-based pages such as the scatter plotter and the draft radial profiles page
Removing Neighborhood Profiles checkpointing
…ethod to get set since it never was since it was being set in the name==main block, which is never called by Multiplex_Analysis_Web_Apps.py
…nfig(layout=wide)'; the problem still occurs: 2024-09-23 13:38:45.780 WARNING streamlit.runtime.scriptrunner_utils.script_run_context: Thread 'MainThread': missing ScriptRunContext! This warning can be ignored when running in bare mode.
…t causes the problem to occur, at least in the MAWA code stack
…) function. It was previously outside it above the import statements because at least one of those scripts contained calls to streamlit (well, to st) outside functions, which can't be called before the layout command
…are detected so there must be no more streamlit calls before layout is called in the main() function in Multiplex_Analysis_Web_Apps.py. However, running the forking test still executes slowly with seconds of overhead.
…ge amount of overhead
…of how parallel calls are made in MAWA. The slow imports still occur the same way, we probably just need to fix those scripts
…b.py are commented out that speed goes back to normal (note in my last commit I still had one of those mistakenly commented out)
…enotyper, will address that later
…hood_profiles import NeighborhoodProfiles, UMAPDensityProcessing' in nidap_dashboard_lib.py is slow
…y... so it seems that umap is what makes anything in nidap_dashboard_lib.py and basic_phenotyper_lib.py slow
…y... so it seems that umap is what makes anything in nidap_dashboard_lib.py and basic_phenotyper_lib.py slow
… still doesn't pop up due to setting the wide layout in the main() function now
…peed of module imports and their effects on the forking testing
Check ubuntu installation + Andrew's additions
…s, though I'm a bit nervous about the consistency of the installation of 'annoy'. But the last two times it worked. This adds Python-based installation of packages after environment.yml/startup.sh have been used to set up the environments.
Update live installation of packages so that both unpublished workspaces and published dashboards work
…aller than the dataframe size; if so, then essentially just return the whole dataframe
… interest in case they have changed and haven't updated through the app
…SIT replace them with underscores; until now, just some of them did, like those in single_roi_outlines_on_whole_slides
Three bug fixes
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Removing security issues