From 2d59ba902ede3f1ff77eeffd80d08cb2f6cb43f2 Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Tue, 31 Aug 2021 10:23:19 +0100 Subject: [PATCH 01/17] Add the install_requires automatically --- setup.py | 40 ++++++++++++++++++++++++++++++++++------ 1 file changed, 34 insertions(+), 6 deletions(-) diff --git a/setup.py b/setup.py index 03ad42dc..6b72ce6d 100644 --- a/setup.py +++ b/setup.py @@ -38,6 +38,12 @@ def run(self): setup( name='snmachine', + author='Michelle Lochner', + author_email='dr.michelle.lochner@gmail.com', + description='Machine learning code for photometric supernova ' + 'classification', + url='https://github.com/LSSTDESC/snmachine', + license='BSD-3-Clause License', use_scm_version={ "root": ".", "relative_to": __file__, @@ -50,10 +56,32 @@ def run(self): 'example_data/example_data_for_tests.pckl']}, exclude_package_data={'utils': ['archive/*']}, cmdclass={'install': ExtractExampleData}, - url='https://github.com/LSSTDESC/snmachine', - license='BSD-3-Clause License', - author='Michelle Lochner', - author_email='dr.michelle.lochner@gmail.com', - description='Machine learning code for photometric supernova ' - 'classification' + install_requires=['astropy>=1.1.2', + 'jupyter>=1.0.0', + 'matplotlib>=1.5.1', + 'numpy>=1.18.4', + 'scikit-learn=0.20.0', + 'scipy>=0.17.0', + 'george>=0.3.0', + 'iminuit==1.2', + 'pandas>=0.23.0', + 'extinction>=0.3.0', + 'imbalanced-learn>=0.4.3', + 'python=3.7', + 'pip>=20.1', + 'emcee>=2.1.0', + 'numpydoc>=0.6.0', + 'pytest-remotedata>=0.3.1', + 'pywavelets>=0.4.0', + 'sncosmo==2.1.0', + 'nose>=1.3.7', + 'future>=0.16', + 'pyyaml>=3.13', + 'pytest-xdist>=1.26.1', + 'seaborn', + 'schwimmbad', + 'cesium', + 'tqdm', + 'lightgbm' + ] ) From 2c72e266419e963a2ef4372fff9ad2770d787a5f Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Tue, 31 Aug 2021 10:36:30 +0100 Subject: [PATCH 02/17] Minor change --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 6b72ce6d..791fa2ce 100644 --- a/setup.py +++ b/setup.py @@ -60,7 +60,7 @@ def run(self): 'jupyter>=1.0.0', 'matplotlib>=1.5.1', 'numpy>=1.18.4', - 'scikit-learn=0.20.0', + 'scikit-learn=0.20.0', 'scipy>=0.17.0', 'george>=0.3.0', 'iminuit==1.2', From bda3d8f67a6e20c927dbd4d9ac296ed732ab4994 Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Tue, 31 Aug 2021 10:45:33 +0100 Subject: [PATCH 03/17] Minor changes --- setup.py | 53 ++++++++++++++++++++++++++--------------------------- 1 file changed, 26 insertions(+), 27 deletions(-) diff --git a/setup.py b/setup.py index 791fa2ce..f149fab2 100644 --- a/setup.py +++ b/setup.py @@ -56,32 +56,31 @@ def run(self): 'example_data/example_data_for_tests.pckl']}, exclude_package_data={'utils': ['archive/*']}, cmdclass={'install': ExtractExampleData}, - install_requires=['astropy>=1.1.2', - 'jupyter>=1.0.0', - 'matplotlib>=1.5.1', - 'numpy>=1.18.4', + install_requires=['astropy>=1.1.2', + 'jupyter>=1.0.0', + 'matplotlib>=1.5.1', + 'numpy>=1.18.4', 'scikit-learn=0.20.0', - 'scipy>=0.17.0', - 'george>=0.3.0', - 'iminuit==1.2', - 'pandas>=0.23.0', - 'extinction>=0.3.0', - 'imbalanced-learn>=0.4.3', - 'python=3.7', - 'pip>=20.1', - 'emcee>=2.1.0', - 'numpydoc>=0.6.0', - 'pytest-remotedata>=0.3.1', - 'pywavelets>=0.4.0', - 'sncosmo==2.1.0', - 'nose>=1.3.7', - 'future>=0.16', - 'pyyaml>=3.13', - 'pytest-xdist>=1.26.1', - 'seaborn', - 'schwimmbad', - 'cesium', - 'tqdm', - 'lightgbm' - ] + 'scipy>=0.17.0', + 'george>=0.3.0', + 'iminuit==1.2', + 'pandas>=0.23.0', + 'extinction>=0.3.0', + 'imbalanced-learn>=0.4.3', + 'python=3.7', + 'pip>=20.1', + 'emcee>=2.1.0', + 'numpydoc>=0.6.0', + 'pytest-remotedata>=0.3.1', + 'pywavelets>=0.4.0', + 'sncosmo==2.1.0', + 'nose>=1.3.7', + 'future>=0.16', + 'pyyaml>=3.13', + 'pytest-xdist>=1.26.1', + 'seaborn', + 'schwimmbad', + 'cesium', + 'tqdm', + 'lightgbm'] ) From 2be8bdee0fda1b492933476c24a1f8e83be80fb9 Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Tue, 31 Aug 2021 10:46:37 +0100 Subject: [PATCH 04/17] Only some packages --- setup.py | 25 +------------------------ 1 file changed, 1 insertion(+), 24 deletions(-) diff --git a/setup.py b/setup.py index f149fab2..fcf98ac5 100644 --- a/setup.py +++ b/setup.py @@ -59,28 +59,5 @@ def run(self): install_requires=['astropy>=1.1.2', 'jupyter>=1.0.0', 'matplotlib>=1.5.1', - 'numpy>=1.18.4', - 'scikit-learn=0.20.0', - 'scipy>=0.17.0', - 'george>=0.3.0', - 'iminuit==1.2', - 'pandas>=0.23.0', - 'extinction>=0.3.0', - 'imbalanced-learn>=0.4.3', - 'python=3.7', - 'pip>=20.1', - 'emcee>=2.1.0', - 'numpydoc>=0.6.0', - 'pytest-remotedata>=0.3.1', - 'pywavelets>=0.4.0', - 'sncosmo==2.1.0', - 'nose>=1.3.7', - 'future>=0.16', - 'pyyaml>=3.13', - 'pytest-xdist>=1.26.1', - 'seaborn', - 'schwimmbad', - 'cesium', - 'tqdm', - 'lightgbm'] + 'numpy>=1.18.4'] ) From 18cbf67154a1184e4f73388170a135e678f9a23c Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Tue, 31 Aug 2021 10:54:43 +0100 Subject: [PATCH 05/17] Add more packages --- setup.py | 26 ++++++++++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index fcf98ac5..b0fa5d08 100644 --- a/setup.py +++ b/setup.py @@ -59,5 +59,27 @@ def run(self): install_requires=['astropy>=1.1.2', 'jupyter>=1.0.0', 'matplotlib>=1.5.1', - 'numpy>=1.18.4'] -) + 'numpy>=1.18.4', + 'scipy>=0.17.0', + 'george>=0.3.0', + 'iminuit==1.2', + 'pandas>=0.23.0', + 'extinction>=0.3.0', + 'imbalanced-learn>=0.4.3', + 'python=3.7', + 'pip>=20.1', + 'emcee>=2.1.0', + 'numpydoc>=0.6.0', + 'pytest-remotedata>=0.3.1', + 'pywavelets>=0.4.0', + 'sncosmo==2.1.0', + 'nose>=1.3.7', + 'future>=0.16', + 'pyyaml>=3.13', + 'pytest-xdist>=1.26.1', + 'seaborn', + 'schwimmbad', + 'cesium', + 'tqdm', + 'lightgbm'] +) \ No newline at end of file From 8d923856b6f7f27b3de0a65c5db32c17cc164aa8 Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Tue, 31 Aug 2021 11:00:35 +0100 Subject: [PATCH 06/17] Fix installs --- setup.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/setup.py b/setup.py index b0fa5d08..6731654a 100644 --- a/setup.py +++ b/setup.py @@ -60,13 +60,14 @@ def run(self): 'jupyter>=1.0.0', 'matplotlib>=1.5.1', 'numpy>=1.18.4', + 'scikit-learn==0.20.0', 'scipy>=0.17.0', 'george>=0.3.0', 'iminuit==1.2', 'pandas>=0.23.0', 'extinction>=0.3.0', 'imbalanced-learn>=0.4.3', - 'python=3.7', + 'python>=3.7', 'pip>=20.1', 'emcee>=2.1.0', 'numpydoc>=0.6.0', From f0c5a49720e666af548a7d759a72488fd6820697 Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Fri, 3 Sep 2021 19:00:51 +0100 Subject: [PATCH 07/17] Add and modify the required files --- requirements.txt | 19 +++++++++++++++++++ setup.py | 17 +++-------------- 2 files changed, 22 insertions(+), 14 deletions(-) create mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..d6a73dec --- /dev/null +++ b/requirements.txt @@ -0,0 +1,19 @@ +###### Requirements without Version Specifiers ###### +iminuit +seaborn +lightgbm +setuptools_scm + +###### Requirements with Version Specifiers ###### +astropy>=1.1.2 +matplotlib>=1.5.1 +numpy>=1.18.4 +scikit-learn==0.20.0 +scipy>=0.17.0 +george>=0.3.0 +pandas>=0.23.0 +pywavelets>=0.4.0 +sncosmo==2.1.0 +nose>=1.3.7 +future>=0.16 +pyyaml>=3.13 \ No newline at end of file diff --git a/setup.py b/setup.py index 6731654a..1987fa02 100644 --- a/setup.py +++ b/setup.py @@ -57,30 +57,19 @@ def run(self): exclude_package_data={'utils': ['archive/*']}, cmdclass={'install': ExtractExampleData}, install_requires=['astropy>=1.1.2', - 'jupyter>=1.0.0', 'matplotlib>=1.5.1', 'numpy>=1.18.4', 'scikit-learn==0.20.0', 'scipy>=0.17.0', 'george>=0.3.0', - 'iminuit==1.2', + 'iminuit', 'pandas>=0.23.0', - 'extinction>=0.3.0', - 'imbalanced-learn>=0.4.3', - 'python>=3.7', - 'pip>=20.1', - 'emcee>=2.1.0', - 'numpydoc>=0.6.0', - 'pytest-remotedata>=0.3.1', 'pywavelets>=0.4.0', 'sncosmo==2.1.0', 'nose>=1.3.7', 'future>=0.16', 'pyyaml>=3.13', - 'pytest-xdist>=1.26.1', 'seaborn', - 'schwimmbad', - 'cesium', - 'tqdm', - 'lightgbm'] + 'lightgbm', + "setuptools_scm"] ) \ No newline at end of file From 573df7633239b1dc9625ccbc700fec14c95d0bfc Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Fri, 3 Sep 2021 19:37:31 +0100 Subject: [PATCH 08/17] Remove the version requirement from scikit-learn --- requirements.txt | 16 ++++++++-------- setup.py | 6 +++--- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/requirements.txt b/requirements.txt index d6a73dec..cc298b01 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,19 +1,19 @@ ###### Requirements without Version Specifiers ###### iminuit -seaborn lightgbm +scikit-learn +seaborn setuptools_scm ###### Requirements with Version Specifiers ###### astropy>=1.1.2 +future>=0.16 +george>=0.3.0 matplotlib>=1.5.1 +nose>=1.3.7 numpy>=1.18.4 -scikit-learn==0.20.0 -scipy>=0.17.0 -george>=0.3.0 pandas>=0.23.0 +pyyaml>=3.13 pywavelets>=0.4.0 -sncosmo==2.1.0 -nose>=1.3.7 -future>=0.16 -pyyaml>=3.13 \ No newline at end of file +scipy>=0.17.0 +sncosmo==2.1.0 \ No newline at end of file diff --git a/setup.py b/setup.py index 1987fa02..59b0f85a 100644 --- a/setup.py +++ b/setup.py @@ -59,7 +59,7 @@ def run(self): install_requires=['astropy>=1.1.2', 'matplotlib>=1.5.1', 'numpy>=1.18.4', - 'scikit-learn==0.20.0', + 'scikit-learn', 'scipy>=0.17.0', 'george>=0.3.0', 'iminuit', @@ -71,5 +71,5 @@ def run(self): 'pyyaml>=3.13', 'seaborn', 'lightgbm', - "setuptools_scm"] -) \ No newline at end of file + 'setuptools_scm'] +) From 6cc755d716a1d9a71db8f70bd9b84c420f8c1cc3 Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Mon, 13 Sep 2021 16:01:54 -0700 Subject: [PATCH 09/17] add examle PyPI upload example --- .github/workflows/pypi.yaml | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 .github/workflows/pypi.yaml diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml new file mode 100644 index 00000000..0041913b --- /dev/null +++ b/.github/workflows/pypi.yaml @@ -0,0 +1,27 @@ +# Setting up github action for pypi + +name: Upload Python Package + +on: + release: + types: [created] + +jobs: + deploy: + runs-on: ubuntu-20.04 + + steps: + - uses: actions/checkout@v2 + - uses: actions/setup-python@v2 + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install setuptools wheel twine + - name: Build and publish + env: + TWINE_USERNAME: __token__ + TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} + run: | + python setup.py sdist bdist_wheel + twine upload dist/* + From 3475a3240dcbbd01aa210b6e2197a789b54e6024 Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Mon, 13 Sep 2021 19:06:58 -0400 Subject: [PATCH 10/17] use testpypi for now for testing --- .github/workflows/pypi.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml index 0041913b..90d0733a 100644 --- a/.github/workflows/pypi.yaml +++ b/.github/workflows/pypi.yaml @@ -23,5 +23,5 @@ jobs: TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} run: | python setup.py sdist bdist_wheel - twine upload dist/* + twine upload -repository testpypi dist/* From 30e72a742c2b86269223235b77d352ade41edecc Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Wed, 15 Sep 2021 13:24:18 -0400 Subject: [PATCH 11/17] add missing - to repository parameter --- .github/workflows/pypi.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml index 90d0733a..5cbd8d80 100644 --- a/.github/workflows/pypi.yaml +++ b/.github/workflows/pypi.yaml @@ -23,5 +23,5 @@ jobs: TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} run: | python setup.py sdist bdist_wheel - twine upload -repository testpypi dist/* + twine upload --repository testpypi dist/* From 7915949a482abf74f99a8f82923dc8a51e16c999 Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Thu, 16 Sep 2021 10:07:02 +0100 Subject: [PATCH 12/17] Temporarily update the secret name in the workflow --- .github/workflows/pypi.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml index 5cbd8d80..45f25d22 100644 --- a/.github/workflows/pypi.yaml +++ b/.github/workflows/pypi.yaml @@ -20,7 +20,7 @@ jobs: - name: Build and publish env: TWINE_USERNAME: __token__ - TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} + TWINE_PASSWORD: ${{ secrets.TESTPYPI_API_TOKEN }} run: | python setup.py sdist bdist_wheel twine upload --repository testpypi dist/* From e048f6632a4171eee3c3867960e0dfe94ac7bc2e Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Fri, 17 Sep 2021 12:16:45 -0400 Subject: [PATCH 13/17] Replace testpypi with pypi We might be ready to use PyPI after testing with testpypi --- .github/workflows/pypi.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml index 45f25d22..0041913b 100644 --- a/.github/workflows/pypi.yaml +++ b/.github/workflows/pypi.yaml @@ -20,8 +20,8 @@ jobs: - name: Build and publish env: TWINE_USERNAME: __token__ - TWINE_PASSWORD: ${{ secrets.TESTPYPI_API_TOKEN }} + TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} run: | python setup.py sdist bdist_wheel - twine upload --repository testpypi dist/* + twine upload dist/* From afec8a9641fc66431d3b901c263a6dac5cb85816 Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Thu, 21 Oct 2021 14:42:52 -0700 Subject: [PATCH 14/17] 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 616e9e1a664ed14debfa4611bd90a72ff1a62222 Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Tue, 4 Jan 2022 11:32:08 -0800 Subject: [PATCH 15/17] 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 9d554d964f7e9a7e6aba933248bd28c08e1e7228 Mon Sep 17 00:00:00 2001 From: Heather Kelly Date: Thu, 6 Jan 2022 08:25:34 -0800 Subject: [PATCH 16/17] 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 abe55bac3154311477f108861274b3e453bc2285 Mon Sep 17 00:00:00 2001 From: Catarina Alves Date: Mon, 24 Jan 2022 14:09:05 +0000 Subject: [PATCH 17/17] 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',