From faf252b33935b7c922a22e89f55a87a3b7fa0686 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 16:34:36 -0600 Subject: [PATCH 01/17] rename tests --- tests/{test_aggregate.py => test_code_aggregate.py} | 0 ..._intercept_gradient.py => test_code_chi_intercept_gradient.py} | 0 ...test_discretized_misfit.py => test_code_discretized_misfit.py} | 0 tests/{test_io.py => test_code_io.py} | 0 ..._joint_density_misfit.py => test_code_joint_density_misfit.py} | 0 tests/{test_metric.py => test_code_metric.py} | 0 tests/{test_residual.py => test_code_residual.py} | 0 tests/{test_all_notebooks.py => test_notebooks.py} | 0 8 files changed, 0 insertions(+), 0 deletions(-) rename tests/{test_aggregate.py => test_code_aggregate.py} (100%) rename tests/{test_chi_intercept_gradient.py => test_code_chi_intercept_gradient.py} (100%) rename tests/{test_discretized_misfit.py => test_code_discretized_misfit.py} (100%) rename tests/{test_io.py => test_code_io.py} (100%) rename tests/{test_joint_density_misfit.py => test_code_joint_density_misfit.py} (100%) rename tests/{test_metric.py => test_code_metric.py} (100%) rename tests/{test_residual.py => test_code_residual.py} (100%) rename tests/{test_all_notebooks.py => test_notebooks.py} (100%) diff --git a/tests/test_aggregate.py b/tests/test_code_aggregate.py similarity index 100% rename from tests/test_aggregate.py rename to tests/test_code_aggregate.py diff --git a/tests/test_chi_intercept_gradient.py b/tests/test_code_chi_intercept_gradient.py similarity index 100% rename from tests/test_chi_intercept_gradient.py rename to tests/test_code_chi_intercept_gradient.py diff --git a/tests/test_discretized_misfit.py b/tests/test_code_discretized_misfit.py similarity index 100% rename from tests/test_discretized_misfit.py rename to tests/test_code_discretized_misfit.py diff --git a/tests/test_io.py b/tests/test_code_io.py similarity index 100% rename from tests/test_io.py rename to tests/test_code_io.py diff --git a/tests/test_joint_density_misfit.py b/tests/test_code_joint_density_misfit.py similarity index 100% rename from tests/test_joint_density_misfit.py rename to tests/test_code_joint_density_misfit.py diff --git a/tests/test_metric.py b/tests/test_code_metric.py similarity index 100% rename from tests/test_metric.py rename to tests/test_code_metric.py diff --git a/tests/test_residual.py b/tests/test_code_residual.py similarity index 100% rename from tests/test_residual.py rename to tests/test_code_residual.py diff --git a/tests/test_all_notebooks.py b/tests/test_notebooks.py similarity index 100% rename from tests/test_all_notebooks.py rename to tests/test_notebooks.py From 7efc458fc24ad8f57b25b941e811c7a54c893add Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 16:44:54 -0600 Subject: [PATCH 02/17] remove notebook deps from setup.py --- setup.py | 5 ----- 1 file changed, 5 deletions(-) diff --git a/setup.py b/setup.py index e148fab..e793ad7 100644 --- a/setup.py +++ b/setup.py @@ -19,12 +19,7 @@ install_requires=[ "scipy", "numpy", - "jupyter", - "holoviews", - "pandas", "landlab>=1.10", - "terrainbento>=1.1", - "plotnine>=0.6.0", ], package_data={"": ["tests/data/*"]}, ) From 51ce44067a127538296765b4e4d35a58ae2dfebe Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 16:45:06 -0600 Subject: [PATCH 03/17] add notebook deps for binder --- scripts/binder/postBuild | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 scripts/binder/postBuild diff --git a/scripts/binder/postBuild b/scripts/binder/postBuild new file mode 100644 index 0000000..591e69a --- /dev/null +++ b/scripts/binder/postBuild @@ -0,0 +1,3 @@ +#!/bin/bash + +pip install jupyter pandas plotnine holoviews terrainbento From 4c674aa34011a7a0811116dd4f557c1803003e93 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 16:45:20 -0600 Subject: [PATCH 04/17] add notebook deps to travis and appveyor --- .travis.yml | 1 + appveyor.yml | 1 + 2 files changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index b524672..bccbac1 100644 --- a/.travis.yml +++ b/.travis.yml @@ -65,5 +65,6 @@ install: - pip install -e . script: - pip install pytest pytest-cov pytest-datadir coveralls +- pip install jupyter pandas plotnine holoviews terrainbento - pytest --cov-report=xml:$(pwd)/coverage.xml after_success: coveralls diff --git a/appveyor.yml b/appveyor.yml index ac3673c..a521313 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -29,6 +29,7 @@ install: - cmd: set PYTHONUNBUFFERED=1 - cmd: conda config --set always_yes yes - cmd: pip install twine pytest pytest-cov pytest-datadir + - cmd: pip install jupyter pandas plotnine holoviews terrainbento - cmd: conda info - cmd: conda list From 466827dd92294a624f968e8f9c30bb9ca3439cca Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 16:49:42 -0600 Subject: [PATCH 05/17] move binder postBuild to correct location --- {scripts/binder => binder}/postBuild | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename {scripts/binder => binder}/postBuild (100%) diff --git a/scripts/binder/postBuild b/binder/postBuild similarity index 100% rename from scripts/binder/postBuild rename to binder/postBuild From a89b61090b711b61bf3b43009e10a0bf1eee8fd1 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 16:58:19 -0600 Subject: [PATCH 06/17] no more binder build file --- binder/postBuild | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 binder/postBuild diff --git a/binder/postBuild b/binder/postBuild deleted file mode 100644 index 591e69a..0000000 --- a/binder/postBuild +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -pip install jupyter pandas plotnine holoviews terrainbento From 216825018f24552124a1a485433a06bcb782afba Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 16:58:28 -0600 Subject: [PATCH 07/17] rename env-dev --- README.md | 2 +- environment-dev.yml => environment.yml | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename environment-dev.yml => environment.yml (100%) diff --git a/README.md b/README.md index bc988cb..64ecc17 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ To install the umami source code version of umami we recommend creating a conda ``` git clone https://github.com/TerrainBento/umami.git cd umami -conda env create -f environment-dev.yml +conda env create -f environment.yml conda activate umami-dev python setup.py install ``` diff --git a/environment-dev.yml b/environment.yml similarity index 100% rename from environment-dev.yml rename to environment.yml From b60466ed361a6db2ce3d293fa4b6efe9eabc344f Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:12:30 -0600 Subject: [PATCH 08/17] restoring name --- README.md | 2 +- environment.yml => environment-dev.yml | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename environment.yml => environment-dev.yml (100%) diff --git a/README.md b/README.md index 64ecc17..bc988cb 100644 --- a/README.md +++ b/README.md @@ -48,7 +48,7 @@ To install the umami source code version of umami we recommend creating a conda ``` git clone https://github.com/TerrainBento/umami.git cd umami -conda env create -f environment.yml +conda env create -f environment-dev.yml conda activate umami-dev python setup.py install ``` diff --git a/environment.yml b/environment-dev.yml similarity index 100% rename from environment.yml rename to environment-dev.yml From 7db010a44cabab84f6479c2dd5c3356830acbfb8 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:13:09 -0600 Subject: [PATCH 09/17] changing location of requirements --- .travis.yml | 6 +++--- appveyor.yml | 4 ---- setup.py | 9 +++++++++ 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index bccbac1..d5a5b37 100644 --- a/.travis.yml +++ b/.travis.yml @@ -64,7 +64,7 @@ install: - pip install numpy - pip install -e . script: -- pip install pytest pytest-cov pytest-datadir coveralls -- pip install jupyter pandas plotnine holoviews terrainbento - pytest --cov-report=xml:$(pwd)/coverage.xml -after_success: coveralls +after_success: + - pip install coveralls + - coveralls diff --git a/appveyor.yml b/appveyor.yml index a521313..70a898c 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -17,7 +17,6 @@ platform: - x64 os: Previous Visual Studio 2015 -# os: Visual Studio 2013 init: - "ECHO %CONDA_INSTALL_LOCN% %CONDA_PY% %HOME% %PLATFORM%" @@ -28,8 +27,6 @@ install: - cmd: conda update --yes --quiet conda - cmd: set PYTHONUNBUFFERED=1 - cmd: conda config --set always_yes yes - - cmd: pip install twine pytest pytest-cov pytest-datadir - - cmd: pip install jupyter pandas plotnine holoviews terrainbento - cmd: conda info - cmd: conda list @@ -41,5 +38,4 @@ test_script: - pytest -vvv artifacts: - # Archive the generated conda package in the ci.appveyor.com build report. - path: 'dist\*' diff --git a/setup.py b/setup.py index e793ad7..ecbec0a 100644 --- a/setup.py +++ b/setup.py @@ -21,5 +21,14 @@ "numpy", "landlab>=1.10", ], + tests_require=[ + "pytest", + "pytest-cov", + "jupyter", + "holoviews", + "pandas", + "plotnine>=0.6.0", + "terrainbento>=1.1", + ], package_data={"": ["tests/data/*"]}, ) From 648555b597f53e0b6c725bda3ff90326d62f8343 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:26:38 -0600 Subject: [PATCH 10/17] adding back postBuild --- binder/postBuild | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 binder/postBuild diff --git a/binder/postBuild b/binder/postBuild new file mode 100644 index 0000000..aa40295 --- /dev/null +++ b/binder/postBuild @@ -0,0 +1,7 @@ +#!/bin/bash + +pip install jupyter +pip install holoviews +pip install pandas +pip install plotnine>=0.6.0 +pip install terrainbento>=1.1 From d828409d542931896a279fce505298a2cd3a3709 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:26:53 -0600 Subject: [PATCH 11/17] changing location of test requirements --- .travis.yml | 2 ++ appveyor.yml | 6 ++++-- setup.py | 10 ---------- 3 files changed, 6 insertions(+), 12 deletions(-) diff --git a/.travis.yml b/.travis.yml index d5a5b37..829207f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -64,6 +64,8 @@ install: - pip install numpy - pip install -e . script: +- pip install pytest pytest-cov +- pip install jupyter pandas plotnine holoviews terrainbento - pytest --cov-report=xml:$(pwd)/coverage.xml after_success: - pip install coveralls diff --git a/appveyor.yml b/appveyor.yml index 70a898c..220ab12 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -27,14 +27,16 @@ install: - cmd: conda update --yes --quiet conda - cmd: set PYTHONUNBUFFERED=1 - cmd: conda config --set always_yes yes + - cmd: pip install pytest + - cmd: pip install jupyter pandas plotnine holoviews terrainbento - cmd: conda info - cmd: conda list build: false test_script: - - pip install numpy" - - pip install -e ." + - pip install numpy + - pip install -e . - pytest -vvv artifacts: diff --git a/setup.py b/setup.py index ecbec0a..42c4532 100644 --- a/setup.py +++ b/setup.py @@ -21,14 +21,4 @@ "numpy", "landlab>=1.10", ], - tests_require=[ - "pytest", - "pytest-cov", - "jupyter", - "holoviews", - "pandas", - "plotnine>=0.6.0", - "terrainbento>=1.1", - ], - package_data={"": ["tests/data/*"]}, ) From eebb43bfbf42443c030e4df4691e777e6036e40c Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:40:26 -0600 Subject: [PATCH 12/17] deleting coveralls --- .coveralls.yaml | 1 - 1 file changed, 1 deletion(-) delete mode 100644 .coveralls.yaml diff --git a/.coveralls.yaml b/.coveralls.yaml deleted file mode 100644 index bc4c39c..0000000 --- a/.coveralls.yaml +++ /dev/null @@ -1 +0,0 @@ -repo_token: GPzz5lrNDJuA4MQNPWFT6gomXijaPZ7bS From e77501b981ebcbaad282fd9b7cf673fd3df0e940 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:40:37 -0600 Subject: [PATCH 13/17] installing umami for binder --- binder/postBuild | 2 ++ 1 file changed, 2 insertions(+) diff --git a/binder/postBuild b/binder/postBuild index aa40295..03cd060 100644 --- a/binder/postBuild +++ b/binder/postBuild @@ -5,3 +5,5 @@ pip install holoviews pip install pandas pip install plotnine>=0.6.0 pip install terrainbento>=1.1 + +pip install -e . From 43c712c1c7fe50c456946351ec62f92bad582266 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:40:47 -0600 Subject: [PATCH 14/17] specifying python version --- environment-dev.yml | 2 +- setup.py | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/environment-dev.yml b/environment-dev.yml index d3035db..6c2d3c2 100644 --- a/environment-dev.yml +++ b/environment-dev.yml @@ -2,7 +2,7 @@ name: umami-dev channels: - conda-forge dependencies: - - python + - python>=3.6 # for development - black - flake8 diff --git a/setup.py b/setup.py index 42c4532..47a18b2 100644 --- a/setup.py +++ b/setup.py @@ -5,6 +5,7 @@ setup( name="umami", + python_requires=">=3.6", version=versioneer.get_version(), cmdclass=versioneer.get_cmdclass(), description="Umami calculates landscape metrics", From d05a9568c59fd3fee38bdfa2a5770949f8325175 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:51:45 -0600 Subject: [PATCH 15/17] add coverage status --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index bc988cb..0904f0c 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,7 @@ [![Build Status](https://travis-ci.org/TerrainBento/umami.svg?branch=master)](https://travis-ci.org/TerrainBento/umami) [![Build status](https://ci.appveyor.com/api/projects/status/0ehba569dttgsuyv?svg=true)](https://ci.appveyor.com/project/kbarnhart/umami) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/TerrainBento/umami/master) +[![Coverage Status](https://coveralls.io/repos/github/TerrainBento/umami/badge.svg?branch=master)](https://coveralls.io/github/TerrainBento/umami?branch=master) # Umami From 375c439fed0183f51878a1645d0088a8e4e1a772 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:52:21 -0600 Subject: [PATCH 16/17] change indentation --- .travis.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 829207f..74cb56a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -68,5 +68,5 @@ script: - pip install jupyter pandas plotnine holoviews terrainbento - pytest --cov-report=xml:$(pwd)/coverage.xml after_success: - - pip install coveralls - - coveralls +- pip install coveralls +- coveralls From 048821ddf2e17cae2119d9377658bf84648faf40 Mon Sep 17 00:00:00 2001 From: Katy Barnhart Date: Sat, 31 Aug 2019 17:56:43 -0600 Subject: [PATCH 17/17] change coveralls location --- .travis.yml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.travis.yml b/.travis.yml index 74cb56a..b04ea8b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -64,9 +64,7 @@ install: - pip install numpy - pip install -e . script: -- pip install pytest pytest-cov +- pip install pytest pytest-cov coveralls - pip install jupyter pandas plotnine holoviews terrainbento - pytest --cov-report=xml:$(pwd)/coverage.xml -after_success: -- pip install coveralls -- coveralls +after_success: coveralls