From 12090365e5e7af4c8439562965b0359b0531d95e Mon Sep 17 00:00:00 2001 From: Renming Liu Date: Sun, 16 Oct 2022 18:03:33 -0400 Subject: [PATCH 1/3] remove old copyright headers --- dance/__init__.py | 1 - dance/data/__init__.py | 1 - dance/datasets/__init__.py | 1 - dance/modules/__init__.py | 1 - dance/modules/multi_modality/__init__.py | 1 - dance/modules/multi_modality/joint_embedding/__init__.py | 1 - dance/modules/multi_modality/match_modality/__init__.py | 1 - dance/modules/multi_modality/predict_modality/__init__.py | 1 - dance/modules/single_modality/__init__.py | 1 - dance/modules/single_modality/clustering/__init__.py | 1 - dance/modules/single_modality/imputation/__init__.py | 1 - dance/modules/spatial/__init__.py | 1 - dance/modules/spatial/cell_type_deconvo/__init__.py | 1 - dance/modules/spatial/spatial_domain/__init__.py | 1 - dance/plotting/__init__.py | 1 - dance/transforms/__init__.py | 1 - dance/transforms/graph_construct.py | 1 - dance/transforms/preprocess.py | 1 - dance/utils/__init__.py | 1 - dance/utils/loss.py | 2 -- dance/utils/metrics.py | 1 - examples/spatial/spatial_domain/louvain.py | 1 - examples/spatial/spatial_domain/spagcn.py | 1 - examples/spatial/spatial_domain/stagate.py | 1 - examples/spatial/spatial_domain/stlearn.py | 1 - 25 files changed, 26 deletions(-) diff --git a/dance/__init__.py b/dance/__init__.py index 4df469f5..f90ccba6 100644 --- a/dance/__init__.py +++ b/dance/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import logging from dance import config diff --git a/dance/data/__init__.py b/dance/data/__init__.py index f6fd38ae..4f0c3c0b 100644 --- a/dance/data/__init__.py +++ b/dance/data/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import os import urllib.request import zipfile diff --git a/dance/datasets/__init__.py b/dance/datasets/__init__.py index 17470731..e69de29b 100644 --- a/dance/datasets/__init__.py +++ b/dance/datasets/__init__.py @@ -1 +0,0 @@ -# Copyright 2022 DSE lab. All rights reserved. diff --git a/dance/modules/__init__.py b/dance/modules/__init__.py index 153c37b4..e69de29b 100644 --- a/dance/modules/__init__.py +++ b/dance/modules/__init__.py @@ -1 +0,0 @@ -# Copyright 2022 DSE lab. All rights reserved. diff --git a/dance/modules/multi_modality/__init__.py b/dance/modules/multi_modality/__init__.py index 17470731..e69de29b 100644 --- a/dance/modules/multi_modality/__init__.py +++ b/dance/modules/multi_modality/__init__.py @@ -1 +0,0 @@ -# Copyright 2022 DSE lab. All rights reserved. diff --git a/dance/modules/multi_modality/joint_embedding/__init__.py b/dance/modules/multi_modality/joint_embedding/__init__.py index 5a899702..80ff4b39 100644 --- a/dance/modules/multi_modality/joint_embedding/__init__.py +++ b/dance/modules/multi_modality/joint_embedding/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. from .dcca import DCCA from .jae import JAE from .scmogcn import ScMoGCNWrapper diff --git a/dance/modules/multi_modality/match_modality/__init__.py b/dance/modules/multi_modality/match_modality/__init__.py index a8a96a9b..fa355d30 100644 --- a/dance/modules/multi_modality/match_modality/__init__.py +++ b/dance/modules/multi_modality/match_modality/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. from .cmae import CMAE from .scmm import MMVAE from .scmogcn import ScMoGCNWrapper diff --git a/dance/modules/multi_modality/predict_modality/__init__.py b/dance/modules/multi_modality/predict_modality/__init__.py index 89835989..643d2677 100644 --- a/dance/modules/multi_modality/predict_modality/__init__.py +++ b/dance/modules/multi_modality/predict_modality/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. from .babel import BabelWrapper from .cmae import CMAE from .scmm import MMVAE diff --git a/dance/modules/single_modality/__init__.py b/dance/modules/single_modality/__init__.py index 17470731..e69de29b 100644 --- a/dance/modules/single_modality/__init__.py +++ b/dance/modules/single_modality/__init__.py @@ -1 +0,0 @@ -# Copyright 2022 DSE lab. All rights reserved. diff --git a/dance/modules/single_modality/clustering/__init__.py b/dance/modules/single_modality/clustering/__init__.py index 1b78979a..9df3daba 100644 --- a/dance/modules/single_modality/clustering/__init__.py +++ b/dance/modules/single_modality/clustering/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. from .graphsc import GraphSC from .scdcc import ScDCC from .scdeepcluster import ScDeepCluster diff --git a/dance/modules/single_modality/imputation/__init__.py b/dance/modules/single_modality/imputation/__init__.py index d964e2c1..eb0e768e 100644 --- a/dance/modules/single_modality/imputation/__init__.py +++ b/dance/modules/single_modality/imputation/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. from .deepimpute import DeepImpute from .graphsci import GraphSCI from .scgnn import scGNN diff --git a/dance/modules/spatial/__init__.py b/dance/modules/spatial/__init__.py index 17470731..e69de29b 100644 --- a/dance/modules/spatial/__init__.py +++ b/dance/modules/spatial/__init__.py @@ -1 +0,0 @@ -# Copyright 2022 DSE lab. All rights reserved. diff --git a/dance/modules/spatial/cell_type_deconvo/__init__.py b/dance/modules/spatial/cell_type_deconvo/__init__.py index 4e56d002..361f9385 100644 --- a/dance/modules/spatial/cell_type_deconvo/__init__.py +++ b/dance/modules/spatial/cell_type_deconvo/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. from .card import Card from .dstg import DSTGLearner from .spatialdecon import SpatialDecon diff --git a/dance/modules/spatial/spatial_domain/__init__.py b/dance/modules/spatial/spatial_domain/__init__.py index f7ad9b92..68d3941c 100644 --- a/dance/modules/spatial/spatial_domain/__init__.py +++ b/dance/modules/spatial/spatial_domain/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. from .louvain import Louvain from .spagcn import SpaGCN from .stagate import Stagate diff --git a/dance/plotting/__init__.py b/dance/plotting/__init__.py index 17470731..e69de29b 100644 --- a/dance/plotting/__init__.py +++ b/dance/plotting/__init__.py @@ -1 +0,0 @@ -# Copyright 2022 DSE lab. All rights reserved. diff --git a/dance/transforms/__init__.py b/dance/transforms/__init__.py index 153c37b4..e69de29b 100644 --- a/dance/transforms/__init__.py +++ b/dance/transforms/__init__.py @@ -1 +0,0 @@ -# Copyright 2022 DSE lab. All rights reserved. diff --git a/dance/transforms/graph_construct.py b/dance/transforms/graph_construct.py index d632e601..7bc32060 100644 --- a/dance/transforms/graph_construct.py +++ b/dance/transforms/graph_construct.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import itertools import os import pickle diff --git a/dance/transforms/preprocess.py b/dance/transforms/preprocess.py index 3aad41e6..e964fc8e 100644 --- a/dance/transforms/preprocess.py +++ b/dance/transforms/preprocess.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import collections import os import pprint diff --git a/dance/utils/__init__.py b/dance/utils/__init__.py index 4ca57c29..aa1e891d 100644 --- a/dance/utils/__init__.py +++ b/dance/utils/__init__.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import math import os import random diff --git a/dance/utils/loss.py b/dance/utils/loss.py index de6eb6ac..b96e9cc3 100644 --- a/dance/utils/loss.py +++ b/dance/utils/loss.py @@ -1,5 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. - import math from typing import * diff --git a/dance/utils/metrics.py b/dance/utils/metrics.py index 05fe3491..9b5f122c 100644 --- a/dance/utils/metrics.py +++ b/dance/utils/metrics.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import random import numpy as np diff --git a/examples/spatial/spatial_domain/louvain.py b/examples/spatial/spatial_domain/louvain.py index 254a3c0a..e6b0233e 100644 --- a/examples/spatial/spatial_domain/louvain.py +++ b/examples/spatial/spatial_domain/louvain.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import argparse from dance.datasets.spatial import SpotDataset diff --git a/examples/spatial/spatial_domain/spagcn.py b/examples/spatial/spatial_domain/spagcn.py index 10c54bf4..00155ee2 100644 --- a/examples/spatial/spatial_domain/spagcn.py +++ b/examples/spatial/spatial_domain/spagcn.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import argparse from sklearn.metrics import adjusted_mutual_info_score diff --git a/examples/spatial/spatial_domain/stagate.py b/examples/spatial/spatial_domain/stagate.py index 66206055..1f2abba6 100644 --- a/examples/spatial/spatial_domain/stagate.py +++ b/examples/spatial/spatial_domain/stagate.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import argparse import scanpy as sc diff --git a/examples/spatial/spatial_domain/stlearn.py b/examples/spatial/spatial_domain/stlearn.py index 13cb4e36..43d833f0 100644 --- a/examples/spatial/spatial_domain/stlearn.py +++ b/examples/spatial/spatial_domain/stlearn.py @@ -1,4 +1,3 @@ -# Copyright 2022 DSE lab. All rights reserved. import argparse import os From c2b10579f988ec93a20bd86db1b0b40e9cd4b990 Mon Sep 17 00:00:00 2001 From: Renming Liu Date: Sun, 16 Oct 2022 18:05:47 -0400 Subject: [PATCH 2/3] fix doc copyright --- docs/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 8579bd08..2c36061f 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -18,7 +18,7 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = 'dance' -copyright = '2022, DANCE Team' +copyright = '(c) 2022, OmicsML' author = 'DANCE Team' release = '1.0.0' From aab99bc89224acfb02ee6bf1650c5a487465e83b Mon Sep 17 00:00:00 2001 From: Renming Liu Date: Sun, 16 Oct 2022 19:03:41 -0400 Subject: [PATCH 3/3] remvoe unnecessary (c), will automatically added when rendering doc --- docs/source/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 2c36061f..287a7205 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -18,7 +18,7 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = 'dance' -copyright = '(c) 2022, OmicsML' +copyright = '2022, OmicsML' author = 'DANCE Team' release = '1.0.0'