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CHANGELOG

v1.0.2 (2024-02-01)

Fix

  • fix: update package name in action file (00c816c)

Unknown

  • Merge pull request #53 from NIDAP-Community/dev

fix: update package name in action file (1ea1b0c)

  • Merge pull request #52 from NIDAP-Community/CDupdate

fix: update package name in action file (3956593)

v1.0.1 (2024-02-01)

Build

  • build: update conda recipe and action file (32f800c)

Documentation

  • docs(version): Automatic development release (0548007)

  • docs: Adding changelog (34b1e0b)

  • docs(version): Automatic development release (184b4f9)

  • docs(version): Automatic development release (b8b41d3)

  • docs(version): Automatic development release (f420a3b)

  • docs(version): Automatic development release (8b5cc98)

Feature

Fix

  • fix: add skip on CI for harmony (55c1c0d)

  • fix: Suppress warning for celldex, move CI handle for test Harmony, add png for page creation (406594a)

  • fix: Revise version format (7992d22)

  • fix: update readme (d8d4013)

Test

  • test: Adding variant for Action skip (b0bea4c)

  • test: update meta.ymal (1abd118)

  • test: update meta.ymal (46ba936)

  • test: mute line42 in test-Process_Raw_Data (75dbd06)

Unknown

  • Merge pull request #51 from NIDAP-Community/dev

Update test files for Harmony and Annotation, add GitHub page image (5c19124)

  • Merge pull request #50 from NIDAP-Community/CDupdate

fix: add skip on CI for harmony (3268a82)

  • Merge pull request #49 from NIDAP-Community/CDupdate

fix: Suppress warning for celldex, move CI handle for test Harmony, a… (30de884)

  • Merge pull request #47 from NIDAP-Community/dev

Update CD (76e59b4)

  • Merge pull request #46 from NIDAP-Community/CDupdate

docs: Adding changelog (7c5bcf2)

  • Merge pull request #45 from NIDAP-Community/dev

Update repo structure for CD implementation (ca27382)

  • Merge pull request #44 from NIDAP-Community/CDupdate

Update repo structure for Continuous Deployment implementation (fab9424)

  • Merge remote-tracking branch 'origin/main' into dev (c850a61)

  • Merge pull request #43 from NIDAP-Community/revert-42-testCD2

Revert "Test cd2" (dbd1511)

  • Revert "Test cd2" (82c3208)

  • Merge pull request #42 from ruiheesi/testCD2

Test cd2 (696718c)

  • Merge pull request #17 from ruiheesi/release_dev

Release dev (93dac20)

  • Merge pull request #16 from ruiheesi/dev

Dev (f094e92)

  • Merge pull request #15 from ruiheesi/testCD2

Test cd2 (89850c1)

  • Merge remote-tracking branch 'origin/dev' into testCD2 (429581c)

  • feat :test (10b3e05)

  • Merge pull request #14 from ruiheesi/dev

Dev (c932c71)

  • Merge pull request #13 from ruiheesi/testCD2

Test cd2 (da01ac7)

  • Merge pull request #12 from ruiheesi/release_dev

Release dev (447457a)

  • Merge pull request #11 from ruiheesi/dev

Dev (e4a2987)

  • Merge pull request #10 from ruiheesi/testCD2

fix: update readme (a3f0d9c)

  • Merge pull request #9 from ruiheesi/release_dev

Release dev (4026e1a)

  • Merge pull request #8 from ruiheesi/dev

Dev (4364548)

  • Merge pull request #7 from ruiheesi/testCD

test: update meta.ymal (fe470f9)

  • Merge pull request #6 from ruiheesi/dev

Dev (4e75a9f)

  • Merge pull request #5 from ruiheesi/testCD

test: update meta.ymal (caed439)

  • Merge pull request #4 from ruiheesi/dev

Dev (9f27de1)

  • Merge pull request #3 from ruiheesi/testCD

test: mute line42 in test-Process_Raw_Data (abef880)

  • Merge pull request #1 from ruiheesi/testCD

feat: enable CD (0194dd9)

  • Merge pull request #38 from NIDAP-Community/main

Updating dev to avoid potential lost of progress (8936388)

  • Merge pull request #37 from NIDAP-Community/8_4_tutorial

8 4 tutorial (c640c8f)

Dev (0b66085)

  • Merge pull request #35 from NIDAP-Community/heatmap_fix

Fix heatmap (49f0486)

  • Fix heatmap (db3ee4e)

  • Merge pull request #34 from NIDAP-Community/release_6_15_test

Update DESCRIPTION file with author info and short package description (31a4d13)

  • Merge pull request #33 from NIDAP-Community/update_DES

Update DESCRIPTION file (df2abd7)

  • Update DESCRIPTION file (5e43253)

  • Adding auto-generated files (14ff346)

  • Merge pull request #31 from NIDAP-Community/release_6_13

Update 6 13 from Alexei (e2297c6)

  • Merge pull request #30 from NIDAP-Community/release_test

Run all unit tests (407ca8f)

  • Merge pull request #28 from NIDAP-Community/main

Update (2891614)

  • Merge pull request #27 from NIDAP-Community/phil_6_6_no_NG

Modify package function load (370522e)

  • Including "NULL" and "seurat_cluster" tests (8cb6a23)

  • Introducing "cluster" variable functionality (e26f2aa)

  • Modify package function load (fe7ad65)

  • Adding auto-generated files (e65ad6b)

  • Merge pull request #26 from NIDAP-Community/release_test

Passed all tests (4a40802)

  • Merge pull request #25 from NIDAP-Community/phil_6_6_no_NG

Run all unit test (4979266)

Conflicts: NAMESPACE tests/testthat/fixtures/downsample_SO.R (d4b92fe)

need to update violinPlot subset function (41f805e)

Conflicts: NAMESPACE R/Combine_and_Renormalize.R R/Filter_and_QC.R R/PCA_and_Normalization.R R/Post_filter_QC_Plots.R tests/testthat/fixtures/NSCLC_Single/NSCLC_Single_Filtered_PCA_Norm_SO_downsample.rds tests/testthat/fixtures/NSCLC_Single/NSCLC_Single_Filtered_SO_downsample.rds tests/testthat/fixtures/NSCLC_Single/NSCLCsingle_Filtered_PCA_Norm_SO_downsample.rds tests/testthat/fixtures/NSCLC_Single/NSCLCsingle_Filtered_SO_downsample.rds tests/testthat/fixtures/PBMC_Single/PBMC_Single_Filtered_PCA_Norm_SO_downsample.rds tests/testthat/fixtures/PBMC_Single/PBMC_Single_Filtered_SO_downsample.rds tests/testthat/fixtures/downsample_SO.R tests/testthat/test_Combine_and_Renormalize.R tests/testthat/test_Filter_and_QC.R tests/testthat/test_PCA_and_Normalization.R tests/testthat/test_Post_Filter_QC.R (92eae54)

Conflicts: NAMESPACE R/Post_filter_QC_Plots.R tests/testthat/test_Post_Filter_QC.R (4fd27d2)

Conflicts: man/Combine_and_Renormalize.Rd man/Post_filter_QC.Rd (159af06)

At line 200, fix syntax error from "=" to "==" (2916381)

  • Fix syntax error

At line 200, fix syntax error from "=" to "==" (d909584)

  • Helper for Recluster, Sprint 7 compliant. (d5181f9)

  • Helper for Recluster, Sprint 7 compliant. (8f28252)

  • New test for Recluster with correct name. (bf252e2)

  • New test for Recluster with correct name. (0d88348)

  • Old file w bad name gone. New file good. (e903ca0)

  • Old file w bad name gone. New file good. (0e0d81e)

  • Re-arranged for new Sprint 7 formatting and functions. (2c07bcb)

  • Re-arranged for new Sprint 7 formatting and functions. (e670fe9)

  • Merge branch 'main' of https://github.com/NIDAP-Community/SCWorkflow into main

need to push updated code to main (20f0ab7)

need to push updated code to main (189075c)

  • push updated scripts to main (ed4b682)

  • push updated scripts to main (f70b090)

  • Restructured according to new requirements (94b0170)

  • Restructured according to new requirements (797d5be)

  • Restructured according to new requirements (495be93)

  • Restructured according to new requirements (7e53872)

  • Restructured according to new requirements (6043df1)

  • Restructured according to new requirements (5efd01d)

  • Restructured according to new requirements (8465a9e)

  • Restructured according to new requirements (75be9d0)

  • Restructured according to new requirements (8c4739b)

  • Restructured according to new requirements (8a39e82)

  • Restructured according to new requirements (2ccad56)

  • Restructured according to new requirements (4770cf7)

  • Restructured according to new requirements (8762e39)

  • Restructured according to new requirements (c21ca07)

  • Restructured according to new requirements (b9dfed4)

  • Restructured according to new requirements (9cc27d3)

  • Restructured according to new requirements (656b12e)

  • Restructured according to new requirements (2989dbe)

  • Restructured according to new requirements (bf8dcb1)

  • Restructured according to new requirements (d11a692)

  • Restructured according to new requirements (95693f6)

  • Restructured according to new requirements (da04b19)

  • Restructured according to new requirements (6dca0bf)

  • Restructured according to new requirements (de6b4da)

  • Restructured according to new requirements (8f4ea59)

  • Restructured according to new requirements (1741342)

  • Restructured according to new requirements (f522e45)

  • Restructured according to new requirements (dc8cfe2)

  • Restructured according to new requirements (b2235b0)

  • Restructured according to new requirements (6f4bd6d)

  • Delete test-DegGeneExpressionMarkers.R

Replaced with newer, renamed version (237eacf)

  • Delete test-DegGeneExpressionMarkers.R

Replaced with newer, renamed version (ee510b7)

  • Accepted changes to Namespace (b0ef9e7)

  • Accepted changes to Namespace (70d880f)

  • Removed ticks on dotplot code (d6599be)

  • Removed ticks on dotplot code (3b4a6e0)

  • Added select to dplyr import (1311aae)

  • Added select to dplyr import (c860639)

  • Merge branch 'main' of https://github.com/NIDAP-Community/SCWorkflow into main (8759676)

  • Merge branch 'main' of https://github.com/NIDAP-Community/SCWorkflow into main (28e310b)

  • Added snapshot file tests to Name clusters (1a0c530)

  • Added snapshot file tests to Name clusters (de98847)

  • Added more snapshot tests to heatmap (3f138a4)

  • Added more snapshot tests to heatmap (1fe2d7b)

  • Additional snapshot file tests for dual labeling (8d92fcf)

  • Additional snapshot file tests for dual labeling (580ab8d)

  • Additional tests to dotplot by metadata (fbc3ada)

  • Additional tests to dotplot by metadata (b7f6c45)

  • Adding expect snapshot file tests to 3D-tSNE plotter (8f33e2b)

  • Adding expect snapshot file tests to 3D-tSNE plotter (661102c)

  • Formatting changes to helper-dual labeling (8f5da99)

  • Formatting changes to helper-dual labeling (266dec8)

  • Formatting changes to helper - Name clusters (5a6079f)

  • Formatting changes to helper - Name clusters (cfc8b69)

  • Formatting changes to helper-Heatmap (abd3f09)

  • Formatting changes to helper-Heatmap (1ca0e49)

  • Formatting changes to helper-dotplot by Metadata (321e619)

  • Formatting changes to helper-dotplot by Metadata (69653cb)

  • Formatting changes to helper 3D-tSNE (8be697c)

  • Formatting changes to helper 3D-tSNE (c1835c2)

  • Formatting changes to Dotplot by Metadata (7dbbc99)

  • Formatting changes to Dotplot by Metadata (d994b6c)

  • Code changes to Name clusters and formatting (70a9fc2)

  • Code changes to Name clusters and formatting (bca98aa)

  • Formatting changes to Heatmap.R (e1bd5c7)

  • Formatting changes to Heatmap.R (f47e847)

  • Add files via upload

replace image file (7bf9b80)

  • Add files via upload

replace image file (542b65d)

  • Update README.md

additional text (700ad07)

  • Update README.md

additional text (2e0feec)

  • Update README.md

Added image. (7694f8d)

  • Update README.md

Added image. (f28a6a7)

  • Add files via upload

Workflow image (f93175b)

  • Add files via upload

Workflow image (433a89d)

Includes tests on all 5 datasets testing type, as well as one test on MouseTEC that tests UMAP instead of default TSNE. (4da52a7)

  • Initial TestThat for Recluster

Includes tests on all 5 datasets testing type, as well as one test on MouseTEC that tests UMAP instead of default TSNE. (da7c560)

  • Initial R4 functionalization. (7558379)

  • Initial R4 functionalization. (84acb8c)

  • Add files via upload

Initial release (3eca944)

  • Add files via upload

Initial release (deafd1c)

  • Add files via upload

Initial release (77b96a6)

  • Add files via upload

Initial release (91b7594)

  • Add files via upload

Initial commit (4a74c89)

  • Add files via upload

Initial commit (9d694ae)

  • Add files via upload

Initial release (fa2e7c3)

  • Add files via upload

Initial release (25d5857)

  • Add files via upload

Initial release (69d1dcf)

  • Add files via upload

Initial release (900ab4c)

  • Delete DEG_Gene_Expression_Markers.R (5496f85)

  • Delete DEG_Gene_Expression_Markers.R (fe406ea)

  • Add files via upload

Initial release (ea9b264)

  • Add files via upload

Initial release (45fd8d2)

  • Add files via upload

Initial release (c2e8e8c)

  • Add files via upload

Initial release (fee817b)

  • Add files via upload

Initial release (55fd6c9)

  • Add files via upload

Initial release (a59a2bc)

  • Add files via upload

Initial release (ad72a95)

  • Add files via upload

Initial release (aac8353)

  • Add files via upload

Initial release (a0c5606)

  • Add files via upload

Initial release (c31a9f2)

Following the orders (6b41c15)

  • Delete Delete.Me

Following the orders (1f82ca7)

  • Add files via upload

DELETE IMMEDIATELY!!! (986326c)

  • Add files via upload

DELETE IMMEDIATELY!!! (ea68f0a)

update function and parameter names. (83fbdd1)

update function and parameter names. (6f46e6e)

Resolve conflicts (7fa7db9)

  • Merge pull request #9 from NIDAP-Community/Rui_resolve_conflict

Resolve conflicts (7839aba)

Phi test (2d5e7ec)

  • Merge pull request #8 from NIDAP-Community/phi_test

Phi test (87fdb1a)

Update Chariou Single R SO and BRCA combin and Renormalize (e851077)

Update Chariou Single R SO and BRCA combin and Renormalize (072096f)

Update Chariou Single R SO and BRCA combin and Renormalize (1a8fbf8)

merging new changes (b8b1eda)

merging new changes (09c8f46)

merging new changes (729b051)

adding NSCLC_Single SOs (152cf11)

adding NSCLC_Single SOs (b0ea506)

adding NSCLC_Single SOs (d83c561)

new error messaging added (b09cb64)

new error messaging added (d266d5e)

new error messaging added (c0aaa1b)

Conflicts: .gitignore DESCRIPTION tests/testthat/test_Filter_and_QC.R (c58b92e)

Conflicts: .gitignore DESCRIPTION tests/testthat/test_Filter_and_QC.R (8a845be)

Conflicts: .gitignore DESCRIPTION tests/testthat/test_Filter_and_QC.R (bb18f4c)

The conda package build requires a NAMESPACE file to be added, which is being ignored during the dev cycle. (e7ac125)

  • NAMESPACE removed from merge

The conda package build requires a NAMESPACE file to be added, which is being ignored during the dev cycle. (0027492)

  • NAMESPACE removed from merge

The conda package build requires a NAMESPACE file to be added, which is being ignored during the dev cycle. (4f3bbc8)

  • Merge pull request #7 from NIDAP-Community/dev_release_dec_13_22

Dev release dec 13 22 (02999db)

  • Merge pull request #7 from NIDAP-Community/dev_release_dec_13_22

Dev release dec 13 22 (6ec32fa)

  • Merge pull request #7 from NIDAP-Community/dev_release_dec_13_22

Dev release dec 13 22 (2e0f434)

Rui (c09fa3f)

  • Merge pull request #6 from NIDAP-Community/rui

Rui (5d3d3b2)

  • Merge pull request #6 from NIDAP-Community/rui

Rui (e71621d)

Adjusted png render method for NIDAP display (33820ce)

  • Merge pull request #5 from NIDAP-Community/initial_filter_qc

Adjusted png render method for NIDAP display (770cb6a)

  • Merge pull request #5 from NIDAP-Community/initial_filter_qc

Adjusted png render method for NIDAP display (12b4ce3)

  • Adjusted png render method for NIDAP display (0b9e4d2)

  • Adjusted png render method for NIDAP display (9968f1f)

  • Adjusted png render method for NIDAP display (747b89a)

  • Merge pull request #4 from NIDAP-Community/initial_filter_qc

Update namespace (bcc1c7f)

  • Merge pull request #4 from NIDAP-Community/initial_filter_qc

Update namespace (61952ec)

  • Merge pull request #4 from NIDAP-Community/initial_filter_qc

Update namespace (ac05afc)

  • Update namespace (fdcfd52)

  • Update namespace (f070d8e)

  • Update namespace (fd74f19)

  • Merge pull request #3 from NIDAP-Community/initial_filter_qc

Added license file (a3a99b6)

  • Merge pull request #3 from NIDAP-Community/initial_filter_qc

Added license file (5c508c3)

  • Merge pull request #3 from NIDAP-Community/initial_filter_qc

Added license file (d5113f3)

  • Added license file (186d183)

  • Added license file (a8bd74c)

  • Added license file (1d7ed13)

  • Merge pull request #2 from NIDAP-Community/initial_filter_qc

remove GenomeInfoDb (fe8164b)

  • Merge pull request #2 from NIDAP-Community/initial_filter_qc

remove GenomeInfoDb (75ae5fd)

  • Merge pull request #2 from NIDAP-Community/initial_filter_qc

remove GenomeInfoDb (8908e24)

  • remove GenomeInfoDb (f3bb0e6)

  • remove GenomeInfoDb (2b32d4e)

  • remove GenomeInfoDb (b27279e)

  • Merge pull request #1 from NIDAP-Community/initial_filter_qc

Initial push with filter and qc, demo (866a648)

  • Merge pull request #1 from NIDAP-Community/initial_filter_qc

Initial push with filter and qc, demo (a30130b)

  • Merge pull request #1 from NIDAP-Community/initial_filter_qc

Initial push with filter and qc, demo (b627f06)

  • Initial push with filter and qc, demo (a843d4d)

  • Initial push with filter and qc, demo (dcd9fef)

  • Initial push with filter and qc, demo (462a39d)

  • Update README.md

Changed package name (acb154c)

  • Update README.md

Changed package name (fdffdf4)