From fbca900059f69f8b3354e2dd898171a940ca4654 Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Thu, 21 Oct 2021 14:42:52 -0700 Subject: [PATCH 1/4] make utils a subpackage of snmachine --- setup.py | 4 ++-- snmachine/snclassifier.py | 2 +- {utils => snmachine/utils}/__init__.py | 0 {utils => snmachine/utils}/archive/collect.pbs | 0 {utils => snmachine/utils}/archive/collect.py | 0 {utils => snmachine/utils}/archive/conquer.pbs | 0 {utils => snmachine/utils}/archive/conquer.py | 0 {utils => snmachine/utils}/archive/create_jobs.py | 0 {utils => snmachine/utils}/archive/divide.pbs | 0 {utils => snmachine/utils}/archive/divide.py | 0 {utils => snmachine/utils}/archive/plasticc_extract_gp.pbs | 0 {utils => snmachine/utils}/archive/plasticc_extract_gp.py | 0 {utils => snmachine/utils}/archive/post_process.py | 0 {utils => snmachine/utils}/archive/run_pipeline.py | 0 {utils => snmachine/utils}/config.yml | 0 {utils => snmachine/utils}/imblearn_augment.py | 0 {utils => snmachine/utils}/plasticc_feature_engineering.py | 0 {utils => snmachine/utils}/plasticc_make_predictions.py | 0 {utils => snmachine/utils}/plasticc_pipeline.py | 2 +- {utils => snmachine/utils}/plasticc_utils.py | 0 20 files changed, 4 insertions(+), 4 deletions(-) rename {utils => snmachine/utils}/__init__.py (100%) rename {utils => snmachine/utils}/archive/collect.pbs (100%) rename {utils => snmachine/utils}/archive/collect.py (100%) rename {utils => snmachine/utils}/archive/conquer.pbs (100%) rename {utils => snmachine/utils}/archive/conquer.py (100%) rename {utils => snmachine/utils}/archive/create_jobs.py (100%) rename {utils => snmachine/utils}/archive/divide.pbs (100%) rename {utils => snmachine/utils}/archive/divide.py (100%) rename {utils => snmachine/utils}/archive/plasticc_extract_gp.pbs (100%) rename {utils => snmachine/utils}/archive/plasticc_extract_gp.py (100%) rename {utils => snmachine/utils}/archive/post_process.py (100%) rename {utils => snmachine/utils}/archive/run_pipeline.py (100%) rename {utils => snmachine/utils}/config.yml (100%) rename {utils => snmachine/utils}/imblearn_augment.py (100%) rename {utils => snmachine/utils}/plasticc_feature_engineering.py (100%) rename {utils => snmachine/utils}/plasticc_make_predictions.py (100%) rename {utils => snmachine/utils}/plasticc_pipeline.py (99%) rename {utils => snmachine/utils}/plasticc_utils.py (100%) diff --git a/setup.py b/setup.py index 59b0f85a..a8e7a98c 100644 --- a/setup.py +++ b/setup.py @@ -1,4 +1,4 @@ -from setuptools import setup +from setuptools import setup, find_packages from setuptools.command.install import install import sys import os @@ -49,7 +49,7 @@ def run(self): "relative_to": __file__, "fallback_version": __FALLBACK_VERSION__}, setup_requires=['setuptools_scm>=3.2.0'], - packages=['snmachine', 'utils'], + packages=find_packages(), include_package_data=True, package_data={'snmachine': ['example_data/SPCC_SUBSET.tar.gz', 'example_data/output_spcc_no_z/features/*.dat', diff --git a/snmachine/snclassifier.py b/snmachine/snclassifier.py index 20f22154..05d31c12 100644 --- a/snmachine/snclassifier.py +++ b/snmachine/snclassifier.py @@ -27,7 +27,7 @@ from sklearn import model_selection from sklearn.model_selection import PredefinedSplit, StratifiedKFold from sklearn.preprocessing import StandardScaler -from utils import plasticc_utils +from . utils import plasticc_utils # This allows the user to easily loop through all possible classifiers choice_of_classifiers = ['svm', 'knn', 'random_forest', 'decision_tree', diff --git a/utils/__init__.py b/snmachine/utils/__init__.py similarity index 100% rename from utils/__init__.py rename to snmachine/utils/__init__.py diff --git a/utils/archive/collect.pbs b/snmachine/utils/archive/collect.pbs similarity index 100% rename from utils/archive/collect.pbs rename to snmachine/utils/archive/collect.pbs diff --git a/utils/archive/collect.py b/snmachine/utils/archive/collect.py similarity index 100% rename from utils/archive/collect.py rename to snmachine/utils/archive/collect.py diff --git a/utils/archive/conquer.pbs b/snmachine/utils/archive/conquer.pbs similarity index 100% rename from utils/archive/conquer.pbs rename to snmachine/utils/archive/conquer.pbs diff --git a/utils/archive/conquer.py b/snmachine/utils/archive/conquer.py similarity index 100% rename from utils/archive/conquer.py rename to snmachine/utils/archive/conquer.py diff --git a/utils/archive/create_jobs.py b/snmachine/utils/archive/create_jobs.py similarity index 100% rename from utils/archive/create_jobs.py rename to snmachine/utils/archive/create_jobs.py diff --git a/utils/archive/divide.pbs b/snmachine/utils/archive/divide.pbs similarity index 100% rename from utils/archive/divide.pbs rename to snmachine/utils/archive/divide.pbs diff --git a/utils/archive/divide.py b/snmachine/utils/archive/divide.py similarity index 100% rename from utils/archive/divide.py rename to snmachine/utils/archive/divide.py diff --git a/utils/archive/plasticc_extract_gp.pbs b/snmachine/utils/archive/plasticc_extract_gp.pbs similarity index 100% rename from utils/archive/plasticc_extract_gp.pbs rename to snmachine/utils/archive/plasticc_extract_gp.pbs diff --git a/utils/archive/plasticc_extract_gp.py b/snmachine/utils/archive/plasticc_extract_gp.py similarity index 100% rename from utils/archive/plasticc_extract_gp.py rename to snmachine/utils/archive/plasticc_extract_gp.py diff --git a/utils/archive/post_process.py b/snmachine/utils/archive/post_process.py similarity index 100% rename from utils/archive/post_process.py rename to snmachine/utils/archive/post_process.py diff --git a/utils/archive/run_pipeline.py b/snmachine/utils/archive/run_pipeline.py similarity index 100% rename from utils/archive/run_pipeline.py rename to snmachine/utils/archive/run_pipeline.py diff --git a/utils/config.yml b/snmachine/utils/config.yml similarity index 100% rename from utils/config.yml rename to snmachine/utils/config.yml diff --git a/utils/imblearn_augment.py b/snmachine/utils/imblearn_augment.py similarity index 100% rename from utils/imblearn_augment.py rename to snmachine/utils/imblearn_augment.py diff --git a/utils/plasticc_feature_engineering.py b/snmachine/utils/plasticc_feature_engineering.py similarity index 100% rename from utils/plasticc_feature_engineering.py rename to snmachine/utils/plasticc_feature_engineering.py diff --git a/utils/plasticc_make_predictions.py b/snmachine/utils/plasticc_make_predictions.py similarity index 100% rename from utils/plasticc_make_predictions.py rename to snmachine/utils/plasticc_make_predictions.py diff --git a/utils/plasticc_pipeline.py b/snmachine/utils/plasticc_pipeline.py similarity index 99% rename from utils/plasticc_pipeline.py rename to snmachine/utils/plasticc_pipeline.py index 863c04ac..7e2d7f82 100755 --- a/utils/plasticc_pipeline.py +++ b/snmachine/utils/plasticc_pipeline.py @@ -27,7 +27,7 @@ #from imblearn.metrics import classification_report_imbalanced # not used at the moment #from imblearn.over_sampling import SMOTE # not used at the moment #from imblearn.pipeline import make_pipeline # not used at the moment -from utils.plasticc_utils import plasticc_log_loss, plot_confusion_matrix +from snmachine.utils.plasticc_utils import plasticc_log_loss, plot_confusion_matrix from sklearn.ensemble import RandomForestClassifier from sklearn.model_selection import train_test_split diff --git a/utils/plasticc_utils.py b/snmachine/utils/plasticc_utils.py similarity index 100% rename from utils/plasticc_utils.py rename to snmachine/utils/plasticc_utils.py From b14e169b95ab256156e8ec2560637cea808528cc Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Tue, 4 Jan 2022 11:32:08 -0800 Subject: [PATCH 2/4] move archive dir back to top of repo to avoid inclusion during install --- {snmachine/utils/archive => archive}/collect.pbs | 0 {snmachine/utils/archive => archive}/collect.py | 0 {snmachine/utils/archive => archive}/conquer.pbs | 0 {snmachine/utils/archive => archive}/conquer.py | 0 {snmachine/utils/archive => archive}/create_jobs.py | 0 {snmachine/utils/archive => archive}/divide.pbs | 0 {snmachine/utils/archive => archive}/divide.py | 0 {snmachine/utils/archive => archive}/plasticc_extract_gp.pbs | 0 {snmachine/utils/archive => archive}/plasticc_extract_gp.py | 0 {snmachine/utils/archive => archive}/post_process.py | 0 {snmachine/utils/archive => archive}/run_pipeline.py | 0 11 files changed, 0 insertions(+), 0 deletions(-) rename {snmachine/utils/archive => archive}/collect.pbs (100%) rename {snmachine/utils/archive => archive}/collect.py (100%) rename {snmachine/utils/archive => archive}/conquer.pbs (100%) rename {snmachine/utils/archive => archive}/conquer.py (100%) rename {snmachine/utils/archive => archive}/create_jobs.py (100%) rename {snmachine/utils/archive => archive}/divide.pbs (100%) rename {snmachine/utils/archive => archive}/divide.py (100%) rename {snmachine/utils/archive => archive}/plasticc_extract_gp.pbs (100%) rename {snmachine/utils/archive => archive}/plasticc_extract_gp.py (100%) rename {snmachine/utils/archive => archive}/post_process.py (100%) rename {snmachine/utils/archive => archive}/run_pipeline.py (100%) diff --git a/snmachine/utils/archive/collect.pbs b/archive/collect.pbs similarity index 100% rename from snmachine/utils/archive/collect.pbs rename to archive/collect.pbs diff --git a/snmachine/utils/archive/collect.py b/archive/collect.py similarity index 100% rename from snmachine/utils/archive/collect.py rename to archive/collect.py diff --git a/snmachine/utils/archive/conquer.pbs b/archive/conquer.pbs similarity index 100% rename from snmachine/utils/archive/conquer.pbs rename to archive/conquer.pbs diff --git a/snmachine/utils/archive/conquer.py b/archive/conquer.py similarity index 100% rename from snmachine/utils/archive/conquer.py rename to archive/conquer.py diff --git a/snmachine/utils/archive/create_jobs.py b/archive/create_jobs.py similarity index 100% rename from snmachine/utils/archive/create_jobs.py rename to archive/create_jobs.py diff --git a/snmachine/utils/archive/divide.pbs b/archive/divide.pbs similarity index 100% rename from snmachine/utils/archive/divide.pbs rename to archive/divide.pbs diff --git a/snmachine/utils/archive/divide.py b/archive/divide.py similarity index 100% rename from snmachine/utils/archive/divide.py rename to archive/divide.py diff --git a/snmachine/utils/archive/plasticc_extract_gp.pbs b/archive/plasticc_extract_gp.pbs similarity index 100% rename from snmachine/utils/archive/plasticc_extract_gp.pbs rename to archive/plasticc_extract_gp.pbs diff --git a/snmachine/utils/archive/plasticc_extract_gp.py b/archive/plasticc_extract_gp.py similarity index 100% rename from snmachine/utils/archive/plasticc_extract_gp.py rename to archive/plasticc_extract_gp.py diff --git a/snmachine/utils/archive/post_process.py b/archive/post_process.py similarity index 100% rename from snmachine/utils/archive/post_process.py rename to archive/post_process.py diff --git a/snmachine/utils/archive/run_pipeline.py b/archive/run_pipeline.py similarity index 100% rename from snmachine/utils/archive/run_pipeline.py rename to archive/run_pipeline.py From 8d88bf1c2ff6663c6c96f9754148c0eb5bc7c32b Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Thu, 6 Jan 2022 08:25:34 -0800 Subject: [PATCH 3/4] reformat utils import to use snmachine --- snmachine/snclassifier.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/snmachine/snclassifier.py b/snmachine/snclassifier.py index 05d31c12..3ea3ff16 100644 --- a/snmachine/snclassifier.py +++ b/snmachine/snclassifier.py @@ -27,7 +27,7 @@ from sklearn import model_selection from sklearn.model_selection import PredefinedSplit, StratifiedKFold from sklearn.preprocessing import StandardScaler -from . utils import plasticc_utils +from snmachine.utils import plasticc_utils # This allows the user to easily loop through all possible classifiers choice_of_classifiers = ['svm', 'knn', 'random_forest', 'decision_tree', From d7644c8786bf6a65ade95f4ee4e82cbf1bd44c46 Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Mon, 24 Jan 2022 14:09:05 +0000 Subject: [PATCH 4/4] Fix deprecated and compatibility issues --- setup.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index a8e7a98c..ed68a7b4 100644 --- a/setup.py +++ b/setup.py @@ -57,10 +57,10 @@ def run(self): exclude_package_data={'utils': ['archive/*']}, cmdclass={'install': ExtractExampleData}, install_requires=['astropy>=1.1.2', - 'matplotlib>=1.5.1', + 'matplotlib>=3.0.0', 'numpy>=1.18.4', 'scikit-learn', - 'scipy>=0.17.0', + 'scipy>=1.4.0', 'george>=0.3.0', 'iminuit', 'pandas>=0.23.0',