From 5a6e350905c974202be2ad73859def154029f43a Mon Sep 17 00:00:00 2001 From: Daochen Zha Date: Sun, 20 Sep 2020 11:32:42 -0500 Subject: [PATCH 1/3] Fix dependency Former-commit-id: 15b52fa868d02ba2906d582c94745d4fe35ea497 [formerly cd8dc875b62e591c7e4367933bb6774c207e4423] [formerly 0bcfc2a6d233897b63ff5ea19c630c3a18e9000e [formerly 5e6d4dbe74c505b8411e940118d80af3c8c4bdf2]] [formerly d6c56756f2e79123e0ff557216b61ab9a64ee7c8 [formerly 94e86fbdd3affc4c3c96a943e7102c9008f7418e] [formerly 676763512153433e296c1c37da220240d27173f8 [formerly a5d987b5db57f5422e66adf3857a9843c141cda5]]] [formerly a12d6e94b178021df2a5bc48b1f760062ac39155 [formerly e7ef205adb5afc28d5249bb140b265be16c220ce] [formerly 2aae28249d4e33c793674764a499bc68d59bfc04 [formerly 96c19bee0be31e1c65b2cfd64881b92297ef8892]] [formerly 5abe70ab1a7d2dd439a3d8075a2e44a731657e68 [formerly b708a1b0bba4d6e6d4b83f3d1741bfd769cf7c79] [formerly 8132402333df668366d6b6055c80dccb37eb62a4 [formerly 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deletions(-) diff --git a/examples/run_pipeline.py b/examples/run_pipeline.py index ea36682..9d8b7cc 100644 --- a/examples/run_pipeline.py +++ b/examples/run_pipeline.py @@ -15,7 +15,7 @@ parser.add_argument('--target_index', type=int, default=6, help='Index of the ground truth (for evaluation)') parser.add_argument('--metric',type=str, default='F1_MACRO', help='Evaluation Metric (F1, F1_MACRO)') -parser.add_argument('--pipeline_path', default=os.path.join(this_path, '../tods/tods/resources/default_pipeline.json'), +parser.add_argument('--pipeline_path', default=os.path.join(this_path, '../tods/resources/default_pipeline.json'), help='Input the path of the pre-built pipeline description') args = parser.parse_args() diff --git a/requirements.txt b/requirements.txt index fa6a44c..3a55551 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,34 +1,3 @@ -scikit-learn==0.22.0 -pytypes==1.0b5 -frozendict==1.2 -numpy>=1.15.4,<=1.18.1 -jsonschema==2.6.0 -requests>=2.19.1,<=2.22.0 -strict-rfc3339==0.7 -rfc3987==1.3.8 -webcolors>=1.8.1,<=1.10 -dateparser>=0.7.0,<=0.7.2 -python-dateutil==2.8.1 -pandas==0.25.0 -typing-inspect==0.5.0 -GitPython>=2.1.11,<=3.0.5 -jsonpath-ng==1.4.3 -custom-inherit>=2.2.0,<=2.2.2 -PyYAML>=5.1,<=5.3 -pycurl>=7.43.0.2,<=7.43.0.3 -pyarrow==0.15.1 -gputil>=1.3.0,<=1.4.0 -pyrsistent>=0.14.11,<=0.15.7 -scipy>=1.2.1,<=1.4.1 -openml==0.10.1 -lightgbm>=2.2.2,<=2.3.0 -opencv-python-headless<=4.1.1.26,>=4.1 -imageio>=2.3.0,<=2.6.0 -pillow==6.2.1 -xgboost>=0.81,<=0.90 -Jinja2==2.9.4 -simplejson==3.12.0 -gitdb2==2.0.6 -e git+https://github.com/tods-doc/d3m@70aeefed6b7307941581357c4b7858bb3f88e1da#egg=d3m -e git+https://github.com/tods-doc/axolotl@af54e6970476a081bf0cd65990c9f56a1200d8a2#egg=axolotl -e git+https://gitlab.com/datadrivendiscovery/common-primitives.git@046b20d2f6d4543dcbe18f0a1d4bcbb1f61cf518#egg=common_primitives diff --git a/setup.py b/setup.py index 589b997..b155e09 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,7 @@ setup( 'nimfa==1.4.0', 'stumpy==1.4.0', 'more-itertools==8.5.0', - 'gitdb==0.6.4' + #'gitdb==0.6.4' ], entry_points = merge_entry_points() From 3925c8dfc33dca279068c9442edae788a2e25e72 Mon Sep 17 00:00:00 2001 From: lhenry15 Date: Sun, 20 Sep 2020 16:00:54 -0500 Subject: [PATCH 2/3] update setup.py Former-commit-id: 27c283bf4d5e1d1da4ba82f5f619f018b233e3ed [formerly e216194cf753be8bc0054ebfd04097c07b5b1987] [formerly 47f47dbf7466350e33297c8c486cd17881ad1346 [formerly d69266ec09928f6b1b891849f29ee6bf7074bb4f]] [formerly a2101feb7a6cfe07199ee101c7e4b677b24fde62 [formerly 5350c28732dafa569a8a3450b6c69b7e8c01f61b] [formerly 38cceebcba7f31cb10245b0d8bfb596b3a671250 [formerly 085378089eeeed59b26c0d9104130b8362b467ca]]] [formerly c3a46dd99017f3be84e009306a2e20629a27f6e9 [formerly 6cfc0c164b2f01334e6821dee3571d262c872585] [formerly 0babbe96957bb5f2c0171ee6b34720c9d468811f [formerly de19ec0e9298a44ddcd42340c6de4f4a9c652390]] [formerly 48441aff918d5ea33ea381f493b126a4a972113e [formerly 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deletion(-) diff --git a/setup.py b/setup.py index b155e09..615c6f8 100644 --- a/setup.py +++ b/setup.py @@ -41,7 +41,6 @@ setup( 'nimfa==1.4.0', 'stumpy==1.4.0', 'more-itertools==8.5.0', - #'gitdb==0.6.4' ], entry_points = merge_entry_points() From f04a2f685fc41f9549684e7a7d0e8ade15056e5c Mon Sep 17 00:00:00 2001 From: lhenry15 Date: Sun, 20 Sep 2020 16:18:16 -0500 Subject: [PATCH 3/3] merge clean and remove install.sh Former-commit-id: cbc4bbc5f636744a0ae984c494312bd3dae401f5 [formerly 25b05af85b6a3e5208fa2dfd3464bb329740a58b] [formerly 0a5c03797c15aa95bf692ef8e19b8e15735db61f [formerly c8404bf380f83fa14038976b2962d1f59e158bdf]] [formerly c863542c4d718024a63d019053f3072ffc13d235 [formerly 4723769779b0b2fe8f4ff0276e759f712aeebd5b] [formerly 0b835fa7d6631b9d6ae1134e7f4d7a16c27e6a90 [formerly ae6854c2dc0d138755331a824227084b667f0083]]] [formerly d128ea904a734e421b5ebe591c254a44806dfe18 [formerly 53c3c66d00facb0e9d459f6a01af7e89fb99039c] [formerly c5c42b1ed0e26a31d4fe829ae84b856e0b95a460 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Former-commit-id: 7d6c289ed738020b6e7ea0035aca11ed6f80880b --- .install.sh | 23 ----------------------- examples/evaluate_default_pipeline.py | 24 ------------------------ 2 files changed, 47 deletions(-) delete mode 100644 .install.sh delete mode 100644 examples/evaluate_default_pipeline.py diff --git a/.install.sh b/.install.sh deleted file mode 100644 index ada87db..0000000 --- a/.install.sh +++ /dev/null @@ -1,23 +0,0 @@ -pip install -r requirements.txt - -cd d3m -pip install -e . -cd .. - -cd tods/common-primitives -pip install -e . -cd ../.. - -cd tods/common-primitives/sklearn-wrap -pip install -e . -cd ../../.. - -cd tods -pip3 install -e . -cd .. - -cd axolotl -pip3 install -e . -pip3 install -e .[cpu] -cd .. - diff --git a/examples/evaluate_default_pipeline.py b/examples/evaluate_default_pipeline.py deleted file mode 100644 index 1c6b7b5..0000000 --- a/examples/evaluate_default_pipeline.py +++ /dev/null @@ -1,24 +0,0 @@ -import pandas as pd - -from searcher import schemas as schemas_utils -from searcher.utils import generate_dataset_problem, evaluate_pipeline - -table_path = 'datasets/yahoo_sub_5.csv' -target_index = 6 # what column is the target - -#table_path = 'datasets/NAB/realTweets/labeled_Twitter_volume_IBM.csv' # The path of the dataset -time_limit = 30 # How many seconds you wanna search -#metric = 'F1' # F1 on label 1 -metric = 'F1_MACRO' # F1 on both label 0 and 1 - -# Read data and generate dataset and problem -df = pd.read_csv(table_path) -dataset, problem_description = generate_dataset_problem(df, target_index=target_index, metric=metric) - -# Load the default pipeline -pipeline = schemas_utils.load_default_pipeline() - -# Run the pipeline -pipeline_result = evaluate_pipeline(problem_description, dataset, pipeline) -print(pipeline_result) -