From 2707cc84449c2dab07d7d60aa119548b5e834c7d Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 5 Jul 2024 08:04:02 +0200 Subject: [PATCH 1/6] WIP add changelog --- CHANGELOG.md | 0 output_mse.h5ad | Bin 20784 -> 0 bytes 2 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 CHANGELOG.md delete mode 100644 output_mse.h5ad diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..e69de29 diff --git a/output_mse.h5ad b/output_mse.h5ad deleted file mode 100644 index 57135a5984114776e959dd313c9a1f8a2d10d3f3..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 20784 zcmeHPJ#ZUE6kgd05s4FQ2#|!o3nW1S|0pH|lLiIbL4o`jCq+8vES;^JNGEZ3%HV>T zl%c|9N|!D@Lqn<36$2e*N|%)B!oJ<_N!Hnmoya?6@ZF5PyKmpU-TUsn{dxOzKNqL2 z9zA^Ou%IiO6$iwi%JRQwxboj?3YWS59x@rEkC3kR=}bmSq`DKJ4?@1vuL&*C@61k5 z3(3jyIYqTtc}3^)Oi0sxg+Ouo$_zd5T|9LW={ocbMNyxRRQ7=zs#KP1l#ykX%5no` zl~&y)FO;`51AQOs@u0d}h#}}}Qm+Su?mQ0iQ zWoDH`mVby!nxyIn#0=_(y5&8P-Sg{#s+9kBl6#OCA(x=Zh(k(#(*D>W*N9(UJK10B zq~?QYT}c1$8w8T}$M#XgxXeJz`9azHk#%0cO1Sp<)7v+1O=YA)Pw=f5bcXFHhjQ^V zO=talg87B{vIlg14*g|&5FaJvpz6d0adY17 z<}0FHd0*2Vors6$y7^X7Ue9TIp7}-+d?>Gvfx(b`GkNQ}!U!E>ywvz4?{R~m?8dI( zVOEVVlAa&EFiLF$X2EK}?;miB0kj*%A&ri17`jVDVmX}VN5_>smh&p^qsA9Px8|YD z{Yu`)@15`Gey|)G0;2w8o$>J{H!NQ z{viYZ>jwF682FDH_}?_}zh&Tm8}wzQ#b(V7oQ4~eLeGu;lH*5JFLt8R?9D49k@tf` zKspOyz2;m}`N)eS$1R2RC~{)2R0-9I z7wWNbj$N-{W}FZp>Sza_IrHZ`%>~^8?)1(F5I22XxlMO1)N}i`<6q z>4nT`)F=D*p+O#oJ;Cp@+Vo2IyMgWPkVe~z^Kxt)?% ztwyW|S}o#=C)MTJ*G{`#TA6)}`;*UuVQ>rH=fOXXv=YaS=}|r>c>lCq^43e=lK1PR^nP!%EGX}nUza zlYN4K>HOdkJHCJe&kGpddp7Yb;ZIO6#n~wWSlBj|*db3fR(Q zpCXW)-*}xja)asE&EHxW$dN>QH+2M`y*$C$^Ke6xNHGFy}wK6KfsYD2?R{`SK$M2 z@Y}M#Tp}K8FYS+FZfw{e#h94vuaMV(wRDosf50J4wnxBZe;XVyg4=A_-)bV>a4+qT zV%TihAH~3#?5~ADm= z+yZXe{`!pmmzfF8SO9$TH_?R?kg z&wWyqyxQl=na5x1o)78-|9iFT&FATKRLp+&$5(U%?01(D{$1_vwxG|W546vt3moWa z5a59RH`+I_wR@ADG;wHp0oBgbzw^E9wQAgg|BYg@X|KSbQjEHaCq_NRmT!(1aAaA< zaigAGgDO53<#Vz;E&o^^x!SUSUMGr<`vo7xAXCf*^HD7EuRjg_zVZu#IjAnZQUp>2 zQUp>2QUp>2_6z|V>s9*ATSorkhZdSywc6C{SL!s1a=zbXyyTYk>Z>kaGgkA4el1Mi%aYY&&F)^VXDKpVKwZ+jURnNb%<+;`^9K~*&<_s)9zTu^-N z-xu`tDb|jECwo~-!e(0+WdDmQ_oCmG+3XjfqgNYv&{2=Q@ox~g*zAqITOmkqF&{;{~Dk^y}E66oA?m9L9G^TdNQ*D!o;`9n(p!%iW_+D?%GbN zh3ws19olv|<)@Mrxog|iK0nQdzUE~&?CGmxU0><9`mC=-=u5BjHNP4D&OzCWN}=C~ z`BPI&_sg1-%K<*c!sU9n=mx(2#ujlhJ@gj5P<}YVLqklDnlg73ZUdXciY=SIDngQhpuKZ91k$4`cXZ}?BX51) gpl?0cutV}ebG&NuyGXsxdz<4`X-R9N|8$h`4_#-kaR2}S From 8d161552fb65acb448fd631dee2185e62e244d05 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 5 Jul 2024 08:09:36 +0200 Subject: [PATCH 2/6] WIP changelog --- CHANGELOG.md | 47 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e69de29..8f12e95 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -0,0 +1,47 @@ +# denoising 0.1.0 + +### MAJOR CHANGES + +* Update to viash 0.9.0 RC6 + + + +## transfer from openproblems-v2 repository + +### NEW FUNCTIONALITY + +* `api/file_*`: Created a file format specifications for the h5ad files throughout the pipeline. + +* `api/comp_*`: Created an api definition for the split, method and metric components. + +* `process_dataset`: Added a component for processing common datasets into task-ready dataset objects. + +* `resources_test/denoising/pancreas` with `src/tasks/denoising/resources_test_scripts/pancreas.sh`. + +* `workflows/run`: Added nf-tower test script. (PR #205) + +### V1 MIGRATION + +* `control_methods/no_denoising`: Migrated from v1. Extracted from baseline method + +* `control_methods/perfect_denoising`: Migrated from v1.Extracted from baseline method + +* `methods/alra`: Migrated from v1. Changed from python to R and uses lg_cpm normalised data instead of L1 sqrt + +* `methods/dca`: Migrated and adapted from v1. + +* `methods/knn_smoothing`: Migrated and adapted from v1. + +* `methods/magic`: Migrated from v1. + +* `metrics/mse`: Migrated from v1. + +* `metrics/poisson`: Migrated from v1. + +### Changes from V1 + +* Anndata layers are used to store data instead of obsm + +* extended the use of sparse data in methods unless it was not possible + +* process_dataset also removes unnecessary data from train and test datasets not needed by the methods and metrics. \ No newline at end of file From 5f7b1000144acb65395a52ebb8b315b515814301 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 5 Jul 2024 09:32:46 +0200 Subject: [PATCH 3/6] Update changelog --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8f12e95..878d191 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,9 +1,10 @@ # denoising 0.1.0 -### MAJOR CHANGES +## BREAKING CHANGES * Update to viash 0.9.0 RC6 +* Directory structure has been updated. ## transfer from openproblems-v2 repository From 18e098715e49176c78e29bb61e4580afcbdb4e4e Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 5 Jul 2024 09:34:36 +0200 Subject: [PATCH 4/6] add PR to changelog --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 878d191..202f073 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,9 @@ * Directory structure has been updated. +## NEW FUNCTIONALITY + +* Add `CHANGELOG.md` (PR #7) ## transfer from openproblems-v2 repository From 07d9ec3d44c024184ba4ada6e4cf18a81bc26b23 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 5 Jul 2024 09:37:20 +0200 Subject: [PATCH 5/6] update changelog --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 202f073..655b532 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,7 +8,11 @@ ## NEW FUNCTIONALITY -* Add `CHANGELOG.md` (PR #7) +* Add `CHANGELOG.md` (PR #7). + +## MINOR CHANGES + +* Remove dtype parameter in `.Anndata()` (PR #6). ## transfer from openproblems-v2 repository From 0921fb09ac6644216da44f481a2b06930acb8bac Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 5 Jul 2024 09:40:16 +0200 Subject: [PATCH 6/6] undo commit --- CHANGELOG.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 655b532..202f073 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,11 +8,7 @@ ## NEW FUNCTIONALITY -* Add `CHANGELOG.md` (PR #7). - -## MINOR CHANGES - -* Remove dtype parameter in `.Anndata()` (PR #6). +* Add `CHANGELOG.md` (PR #7) ## transfer from openproblems-v2 repository