From f82c81ef66482e1d90321425fd7318401558fc7c Mon Sep 17 00:00:00 2001 From: daniel-rijsketic Date: Mon, 24 Jun 2024 13:28:13 -0600 Subject: [PATCH] make htmll --- .../docs/_build/doctrees/environment.pickle | Bin 5710332 -> 5710484 bytes .../docs/_build/doctrees/installation.doctree | Bin 25927 -> 26079 bytes .../_build/html/_sources/installation.md.txt | 2 ++ unravel/docs/_build/html/installation.html | 2 ++ unravel/docs/_build/html/searchindex.js | 2 +- unravel/docs/installation.md | 2 ++ 6 files changed, 7 insertions(+), 1 deletion(-) diff --git a/unravel/docs/_build/doctrees/environment.pickle b/unravel/docs/_build/doctrees/environment.pickle index d651a10c0e39eadf6e326b7479a7a38ee356c860..7869bf24919d40ecd91b97376fed06545471c19a 100644 GIT binary patch delta 9241 zcmb_id0bTG`uEIoW?_H|(%25y$Gk=w6i*}U+eSxP9 z1j;r`C9`u&%cX3&*IcV>*EG!*%`z-Yy&C-9=bV{w?AN`2{rY@{`JQKcpXYg>_xm2O z8}EK0Y2N>ZWScF6q|b^bhqA*-S57+Pf~f70u}mD4#l(9U3;1SPEKD;z9_ukl8q83i zZ8S@p8)AujypEil9Z7!9Fu}G6my8_Ah*ikvE~zZ9XeO8DTF94~iLmbxt6o;Hu&|l* zlp9I@@PcUVlIlfe_f{-OnX_MOH{Oqp#W zd+*Va_Q?@cm;}Ck3NPu%b1)|G&9mvH)SJ9B(o6Q0St1(30)a6m_&zinHsr)GX0o?j zPfGJxCI*;CWAymNx?-4SQZmyaX>gO3*#v_z}8W5 zEXmKd!=h-1ogAK^AodY<#tIu>HP}gNslBz(X_qu4fcuIyi5$%^!p!jzY7&#*~+T9%?Q1g^gCY@I< z)N2unCeA!L`6a_f9vW?g)Qb^nNrRQ_9jPO;a#W0qA`97?sU$~>qT#0)lZLeCX~i?&d|G*&Cjq_EE|`SGKlm-g$|pc3*)UbMKbnd?D8WM%c@y0Qfe%IYc? 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Installing UNRAVEL on Linux or WSL
cd <path/to/repo/clone>
 
 git pull  # This will update the local repo
+
+pip install -e .  # This will update commands and install new dependencies
diff --git a/unravel/docs/_build/html/searchindex.js b/unravel/docs/_build/html/searchindex.js index 25e4e1ef..343bd78e 100644 --- a/unravel/docs/_build/html/searchindex.js +++ b/unravel/docs/_build/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"3 letter orientation code": [[0, null]], "Add images to sample?? dirs": [[0, "add-images-to-sample-dirs"]], "Additional contributions from": [[1, "additional-contributions-from"]], "All commands": [[0, null]], "Allen brain atlas coloring": [[0, null]], "Analysis steps": [[0, "analysis-steps"]], "Automatic logging of scripts": [[0, null]], "Back up raw data": [[0, "back-up-raw-data"]], "Background subtraction": [[0, null]], "Batch stitching settings": [[0, null]], "CLI usage:": [[96, "cli-usage"]], "Cluster correction": [[0, "cluster-correction"]], "Cluster validation": [[0, "cluster-validation"]], "Common commands": [[0, "common-commands"]], "Contact us": [[1, "contact-us"]], "Contents:": [[1, null]], "Data can be distributed across multiple drives": [[0, null]], "Define common variables in a shell script": [[0, "define-common-variables-in-a-shell-script"]], "Developers": [[1, "developers"]], "Editing .bashrc or .zshrc": [[2, "editing-bashrc-or-zshrc"]], "Example experiment folder structure after analysis": [[0, "example-experiment-folder-structure-after-analysis"]], "Example sample?? folder structure after analysis": [[0, "example-sample-folder-structure-after-analysis"]], "Getting started": [[1, "getting-started"]], "Guide": [[0, "guide"]], "Help on commands": [[0, "help-on-commands"]], "Helper Functions:": [[28, "helper-functions"]], "If sample orientations vary": [[0, null]], "Indices": [[1, "indices"]], "Installation": [[2, "installation"]], "Installing UNRAVEL on Linux or WSL": [[2, "installing-unravel-on-linux-or-wsl"]], "Listing commands": [[0, "listing-commands"]], "Log exp paths, commands, etc.": [[0, "log-exp-paths-commands-etc"]], "Main Functions:": [[28, "main-functions"]], "Main dependencies": [[1, "main-dependencies"]], "Make a sample_key.csv:": [[0, "make-a-sample-key-csv"]], "Make an exp_notes.txt": [[0, null]], "Make sample folders": [[0, "make-sample-folders"]], "Module contents": [[75, "module-contents"]], "More info on commands": [[0, null]], "Name sample folders like sample01, sample02, \u2026": [[0, null]], "Note x/y and z voxel sizes": [[0, "note-x-y-and-z-voxel-sizes"]], "Open source options for stitching": [[0, null]], "Optional: clean tifs": [[0, "optional-clean-tifs"]], "Overview and steps for voxel-wise stats": [[0, null]], "Python usage:": [[65, "python-usage"], [96, "python-usage"]], "Region-wise stats": [[0, "region-wise-stats"]], "Registration": [[0, "registration"]], "Running batch stitching": [[0, null]], "Segmentation": [[0, "segmentation"]], "Set up": [[0, "set-up"]], "Setting Up Windows Subsystem for Linux (WSL)": [[2, "setting-up-windows-subsystem-for-linux-wsl"]], "Sorting by hierarchy and volume:": [[23, "sorting-by-hierarchy-and-volume"]], "Stitch z-stacks": [[0, "stitch-z-stacks"]], "Subpackages": [[75, "subpackages"]], "Support is welcome for": [[1, "support-is-welcome-for"]], "Syntax": [[0, null]], "T-test usage:": [[20, "t-test-usage"]], "Todo": [[0, "id1"], [0, "id2"], [0, "id5"], [2, "id1"]], "Train an Ilastik project": [[0, "train-an-ilastik-project"], [0, null]], "Tukey\u2019s test usage:": [[20, "tukey-s-test-usage"]], "Typical workflow": [[0, "typical-workflow"]], "UN-biased high-Resolution Analysis and Validation of Ensembles using Light sheet images": [[1, "un-biased-high-resolution-analysis-and-validation-of-ensembles-using-light-sheet-images"]], "UNRAVEL visualizer": [[1, "unravel-visualizer"]], "Usage": [[3, "usage"], [6, "usage"], [7, "usage"], [9, "usage"], [11, "usage"], [12, "usage"], [13, "usage"], [14, "usage"], [15, "usage"], [17, "usage"], [18, "usage"], [19, "usage"], [61, "usage"]], "Usage for Tukey\u2019s tests w/ reordering and renaming of conditions:": [[62, "usage-for-tukey-s-tests-w-reordering-and-renaming-of-conditions"]], "Usage for activating sample?? dirs for certain conditions:": [[83, "usage-for-activating-sample-dirs-for-certain-conditions"]], "Usage for checking which clusters are present if the min cluster size was 100 voxels:": [[58, "usage-for-checking-which-clusters-are-present-if-the-min-cluster-size-was-100-voxels"]], "Usage for forward warping atlas to tissue space:": [[98, "usage-for-forward-warping-atlas-to-tissue-space"]], "Usage for inverse warping tissue to atlas space:": [[98, "usage-for-inverse-warping-tissue-to-atlas-space"]], "Usage for printing all non-zero intensities:": [[58, "usage-for-printing-all-non-zero-intensities"]], "Usage for printing the number of voxels for each intensity that is present:": [[58, "usage-for-printing-the-number-of-voxels-for-each-intensity-that-is-present"]], "Usage for renaming directories:": [[81, "usage-for-renaming-directories"]], "Usage for renaming files:": [[81, 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"wirefram": 48, "wise": 0, "workflow": 0, "wsl": 2, "x": 0, "y": 0, "z": [0, 35, 94], "z_score": 94, "zarr_to_nii": 44, "zero": [58, 84], "zshrc": 2}}) \ No newline at end of file diff --git a/unravel/docs/installation.md b/unravel/docs/installation.md index 6bac9e7e..278ca4bd 100644 --- a/unravel/docs/installation.md +++ b/unravel/docs/installation.md @@ -127,6 +127,8 @@ pip install unravel cd git pull # This will update the local repo + + pip install -e . # This will update commands and install new dependencies ``` ## Editing .bashrc or .zshrc