angelolab / ark-analysis

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• 0.3.0
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• gh-readonly-queue/main/pr-973-79177931bdfaa98cae63b0a33c6aee289f93fc9a
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• gh-readonly-queue/main/pr-999-e663b04156d6b5e299d33a48dfc3314df6601d5d
• git_install_instructions
• github-actions-from-template
• global-settings
• google-drive-documentation
• google-drive-hotfix
• google-drive-integration
• ignore_hidden_files
• improve_jupyter_launch
• initial_deploy
• input_validation
• integrated_plotting
• integrated_plotting_function
• integrated_plotting_functions
• ipympl_fix
• iter_viz
• iterable_dtypes_fix
• jitter_signal
• jupyter_lab
• k_means
• k_means_mat
• kmeans_neighborhood_nb_update
• kmeans_nh_no_excluded_channels_fix
• kmeans_seed
• landing_doc
• lda_metrics
• line-length-fix
• line_length
• load_tree_wrong_chan_name
• load_utils/load_tif
• load_utils_fix
• load_utils_float_conversion_warning
• local-updating
• localize-mibitiff
• low_contrast_warning
• m1_ark_setup
• main
• mantis/generalize_seg_mask_suffix
• mantis/img_suffix
• mantis_assign_cells
• mantis_dir
• mantis_seg_suffix
• marker_verify
• mask_index_fix
• master
• meta_dup
• meta_zscore_slider
• metacluster_gui
• metacluster_width
• mibilib-workaround
• mibitiff-throw-error
• mibitiff_cell_mat
• mixing_score
• modify_nuc_labels
• morph_add
• morph_doc
• morph_index_fix
• move_meta_rename
• multiarch_docker
• nbsphinx_delete
• neigh_index
• neighbor_notebook
• neighborhood_progress
• new_cluster_boost
• new_rand_mod
• new_som
• next_release_v0.4.1
• next_release_v0.4.2
• next_release_v0.4.3
• next_release_v0.4.4
• next_release_v0.5.0
• next_release_v0.5.1
• ngreenwald-patch-1
• ngreenwald-patch-1-1
• no-contrast-check
• normal_transform
• notebook_reorg
• notebook_tests
• notebook_update_test_bash_cmd
• nuc_filter
• nuc_memb_viz
• nuclear_counts_false
• nuclear_fix
• nuclei_split_threshold
• ome_tiff
• optimization/compressed_csvs
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• overlay_cmap
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• parallel_som
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• pixel_mask_batches
• pixel_mask_boost
• pixel_mask_index
• pixel_overlay_patch
• pixel_path_fix
• pixel_som_verify_fix
• pixie/filter_with_nuclear_mask
• pixie_authorship
• pixie_clean
• plot_clustering_result
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• point_remove
• post_clustering
• preprocess_pixie_cell
• processing_branch
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• propagate_fovs
• py_consensus
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• pypi_bugfix
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• pypi_name
• pypi_req_fix
• pypi_setup
• python-3.6
• python-3.7
• python-3.8+AppleSilicon_support
• python_3.7
• python_3.7_version_download_fix
• qc_metric_moly
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• r_som
• rand_mod
• readd_docker_update
• readme-clarification
• readme/pipeline_flowchart/pixie
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• regionprops_extension
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• sphinx_setup
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• v0.4.0
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• v0.4.4
• v0.5.0
• v0.5.1
• validate_path_update
• validate_paths_usage
• verify_err_msg
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• virt_env_doc
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• xarray_exp
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• zip_compression

Build # 1187

Build Type

push

travis-ci-com

Committed by web-flow

Commit Message

Set up documentation using Sphinx (#178)

* Initial directory setup of Sphinx

* Add missing folders to docs directory

* Fix requirements.txt typo for recommonmark

* Add HTML directory from Makefile

* Remove sphinxcontrib from requirements.txt

* Update with more detailed examples and parsing

* Remove extraneous files from _build

* Add /_build to the .gitignore so it won't try to commit files from there (use Makefile to generate them OYO)

* Add more config parameters and libraries needed to requirements.txt

* Update index.rst to handle new Markdown files

* Add _markdown files used to generate code

* Add more files to markdown generated

* Fix annoying numpy.core.multiarray import error and add mock library to requirements.txt

* Remove extraneous markdown files and separate documentation-specific libraries into separate requirements.txt file

* Check what happens when requirements.txt is re-added

* Fix requirements and add new markdown without module content

* Add xarray intersphinx (still need to address potential issues with this), mostly to see if readthedocs now passes

* Forgot to add ipython to rtd-requirements.txt

* Make description in ark.analysis.md clearer

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