From 1a40417b7d93cde6a25e3ce8d5282b13f477ca8a Mon Sep 17 00:00:00 2001 From: Michael Welborn Date: Fri, 21 Nov 2025 13:49:57 -0600 Subject: [PATCH 1/8] Update dependencies, notably `indico-toolkit` to 7.2.2 --- groundtruth/samples.py | 4 +- poetry.lock | 673 +++++++++++++++++++++++------------------ pyproject.toml | 36 +-- tests/test_samples.py | 5 +- 4 files changed, 399 insertions(+), 319 deletions(-) diff --git a/groundtruth/samples.py b/groundtruth/samples.py index 80270d7..cdddefa 100644 --- a/groundtruth/samples.py +++ b/groundtruth/samples.py @@ -169,8 +169,8 @@ def label_or_model(prediction: Prediction) -> str: return ( prediction.label if isinstance(prediction, Extraction) - else prediction.model.name - ) + else prediction.task.name + ) # fmt: skip def text_or_label(prediction: Prediction) -> str: diff --git a/poetry.lock b/poetry.lock index 2ac954d..ce442d7 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.4 and should not be changed by hand. 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"typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"}, ] -markers = {main = "python_version < \"3.11\""} +markers = {main = "python_version == \"3.10\""} [[package]] name = "typish" @@ -1837,4 +1918,4 @@ multidict = ">=4.0" [metadata] lock-version = "2.1" python-versions = ">=3.10,<4" -content-hash = "6f18d9651d75c8fcd19fdbebd9b4a5b1b40bc52d97f546626eeb9d8ad8acaa4b" +content-hash = "939a4d023084543bbf45391bb9ad31ff088ca224cea0c41842b30e4cb9452a1d" diff --git a/pyproject.toml b/pyproject.toml index db298d8..4c5306c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,30 +13,30 @@ readme = "README.md" requires-python = ">=3.10,<4" version = "1.3.0" dependencies = [ - "aiometer (>=0.5.0,<0.6)", - "arguably (>=1.3.0,<2)", - "indico-client (>=6.14.0,<7)", - "indico-toolkit (>=6.14.0,<7)", - "munkres (>=1.1.4,<2)", - "pathvalidate (>=3.2.1,<4)", - "polars (>=1.8.2,<2)", - "rapidfuzz (>=3.12.2,<4.0.0)", - "rich (>=13.9.1,<14)", + "aiometer (>=1.0.0,<2.0.0)", + "arguably (>=1.3.0,<2.0.0)", + "indico-client (>=6.14.1,<7.0.0)", + "indico-toolkit (>=7.2.2,<8.0.0)", + "munkres (>=1.1.4,<2.0.0)", + "pathvalidate (>=3.3.1,<4.0.0)", + "polars (>=1.35.2,<2.0.0)", + "rapidfuzz (>=3.14.3,<4.0.0)", + "rich (>=14.2.0,<15.0.0)", ] [tool.poetry.group.dev.dependencies] -black = "^25.1.0" -coverage = "^7.6.12" -mypy = "^1.15.0" -pytest = "^8.3.4" -pytest-asyncio = "^0.25.3" -pytest-cov = "^6.0.0" -pytest-mock = "^3.14.0" -ruff = "^0.9.6" +black = "^25.11.0" +coverage = "^7.12.0" +mypy = "^1.18.2" +pytest = "^9.0.1" +pytest-asyncio = "^1.3.0" +pytest-cov = "^7.0.0" +pytest-mock = "^3.15.1" +ruff = "^0.14.6" [tool.poetry.requires-plugins] poetry-plugin-shell = "^1.0.0" -poethepoet = {extras = ["poetry-plugin"], version = "^0.33.0"} +poethepoet = {extras = ["poetry-plugin"], version = "^0.37.0"} [tool.poetry.scripts] groundtruth = "groundtruth.cli:main" diff --git a/tests/test_samples.py b/tests/test_samples.py index 09944ec..2b2e9d7 100644 --- a/tests/test_samples.py +++ b/tests/test_samples.py @@ -124,7 +124,7 @@ def default_extraction( ) -> DocumentExtraction: return DocumentExtraction( document=None, # type: ignore[arg-type] - model=None, # type: ignore[arg-type] + task=None, # type: ignore[arg-type] review=review, label=label, confidences={label: confidence}, @@ -146,10 +146,9 @@ def test_sample() -> None: ) result = Result( - version=1, submission_id=123, documents=tuple(), - models=tuple(), + tasks=tuple(), predictions=PredictionList( ( default_extraction( From bd0bb7ebcbf129e265f3a8ce380de560188c81ac Mon Sep 17 00:00:00 2001 From: Michael Welborn Date: Fri, 21 Nov 2025 13:50:42 -0600 Subject: [PATCH 2/8] Add Python 3.14 to GitHub Actions matrix --- .github/workflows/python.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 862ed55..f5bad97 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12", "3.13"] + python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"] steps: - name: Checkout Commit From c2dcd6a1838a776f8c3c7182cf2192e3c4620d81 Mon Sep 17 00:00:00 2001 From: Michael Welborn Date: Fri, 21 Nov 2025 13:51:11 -0600 Subject: [PATCH 3/8] Skip unnecessary `SubmissionResult()` API call --- groundtruth/workflows.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/groundtruth/workflows.py b/groundtruth/workflows.py index 8fc0caa..9203519 100644 --- a/groundtruth/workflows.py +++ b/groundtruth/workflows.py @@ -8,7 +8,6 @@ from indico.queries import ( GetSubmission, RetrieveStorageObject, - SubmissionResult, WorkflowSubmission, ) @@ -73,8 +72,7 @@ def retrieve_results( # type: ignore[no-any-unimported] ) continue - submission_result = client.call(SubmissionResult(submission, wait=True)) - result = client.call(RetrieveStorageObject(submission_result.result)) + result = client.call(RetrieveStorageObject(submission.result_file)) sanitized_file_name = sanitize(file_name) result_file = Path(sanitized_file_name + ".json") From 609d327b5960665a794228a6b707c1694fbb421d Mon Sep 17 00:00:00 2001 From: Michael Welborn Date: Fri, 21 Nov 2025 13:51:32 -0600 Subject: [PATCH 4/8] Update readme --- README.md | 123 +++++++++++++++++++++++++++++++++--------------------- 1 file changed, 76 insertions(+), 47 deletions(-) diff --git a/README.md b/README.md index d79396b..e6fbe18 100644 --- a/README.md +++ b/README.md @@ -11,13 +11,12 @@ Requires Python ^3.10 and Poetry ^2.0 ``` shell $ poetry install $ poetry poe {format,check,test,all} -$ poetry groundtruth --help +$ poetry run groundtruth --help ``` **CAVEATS:** -- This program only works with extraction models. -- This program requires results to be in file version 1 format. -- This program does not work with bundled submissions or unbundling workflows. +- This program requires results to be in file version 3 format. +- This program requires results to be from a workflow on IPA 7.2 or later. - This program requires Auto Review to be enabled for the workflow. ## Analysis Process @@ -36,57 +35,89 @@ review URLs of the submitted documents will be written to a CSV for future refer groundtruth submit \ --host try.indico.io --token indico_api_token.txt \ --workflow-id 1234 --documents-folder documents \ - --submission-ids-file ground_truth_submission_ids.csv + --submission-ids-file submission_ids.csv ~~~ -At this point, all of the submissions listed in the `ground_truth_submission_ids.csv` -will be queued for processing. Once processed, they should all be manually reviewed to -establish ground truth. After all reviews have been completed, the results can be -downloaded using the `retrieve` command. +Once all submissions have been processed and auto reviewed, download the auto reviewed +result files with the `retrieve` command. These contain the predictions to be compared +against ground truth later. ~~~ shell groundtruth retrieve \ --host try.indico.io --token indico_api_token.txt \ - --submission-ids-file ground_truth_submission_ids.csv \ - --results-folder ground_truth_results + --submission-ids-file submission_ids.csv \ + --results-folder auto_reviews ~~~ -These results contain the ground truths *and* predictions for the first round of ground -truth analysis. Ground truths and prediction samples for a specific model can be -extracted from the results using the `extract` command. +Failed submissions will be logged and may be retried with the `retry` command. + +~~~ shell +groundtruth retry \ + --host try.indico.io --token indico_api_token.txt \ + --submission-ids-file submission_ids.csv +~~~ + +Now review all submissions in Indico to capture the ground truth "answer key." You may +use the review URLs in `submissions_ids.csv` to navigate to them directly. + +Once all submissions have been reviewed, download the HITL reviewed result files. These +contain the ground truths to be compared. + +~~~ shell +groundtruth retrieve \ + --host try.indico.io --token indico_api_token.txt \ + --submission-ids-file submission_ids.csv \ + --results-folder ground_truths +~~~ + +Extract the labels, values, and confidences for `auto_reviews` and `ground_truths` with +the `extract` command. Combine the output CSVs with the `combine` command. This will +automatically match predictions and ground truths by similarity. + +~~~ shell +groundtruth extract \ + --results-folder auto_reviews \ + --samples-file auto_reviews.csv +~~~ ~~~ shell groundtruth extract \ - --results-folder ground_truth_results \ - --extractions-file ground_truth_extractions.csv \ - --model "Invoice Extraction Model" + --results-folder ground_truths \ + --samples-file ground_truths.csv +~~~ + +~~~ shell +groundtruth combine \ + --ground-truths-file ground_truths.csv \ + --predictions-file auto_reviews.csv \ + --combined-file samples.csv ~~~ -At this point, the ground truth/prediction samples in `ground_truth_extractions.csv` -should be manually reviewed to set the `accurate` column to `TRUE` for any samples that -should be considered accurate but that were not identical. The `edit_distance` and -`similarity` columns can be used to bubble up to the top of the extractions file -samples that are likely to be accurate. Any corrections to the selected ground truth -values should also be made in the `ground_truth` column to be used for this and future -rounds of analysis. +At this point, the samples in `samples.csv` should be manually reviewed to set the +`accurate` column to `TRUE` for any ground truth/prediction pairs that should be +considered accurate but whose values were not character-for-character identical. The +`edit_distance` and `similarity` columns can be used to bubble up to the top of the +samples file values that are likely to be accurate. Any corrections to the selected +ground truth values should also be made in the `ground_truth` column to be used for +future rounds of analysis. -After manual review and correction, the extractions file can be analyzed using the -`analyze` command to produce accuracy, volume, and STP performance metrics for a range -of confidence thresholds. Any samples that should not be included in the analysis -(such as ground truths with no value) should be filtered out of the extractions file -prior to analyzing it. +After manual review and correction, the samples file can be analyzed using the `analyze` +command to produce accuracy, volume, and STP performance metrics for a range of +specified confidence thresholds. Any samples that should not be included in the +analysis (such as ground truths with no value) should be filtered out of the +samples file prior to analyzing it. ~~~ shell groundtruth analyze \ - --extractions-file ground_truth_extractions.csv \ - --analysis-file ground_truth_analysis.csv \ + --samples-file samples.csv \ + --analysis-file analysis.csv \ 0.85 0.95 0.99 0.99999 ~~~ Additional rounds of analysis can be performed after model remediation or auto review enhancements have been made to determine the performance impact. Use the `submit`, `retrieve`, and `extract` commands to process the same folder of documents through the -updated workflow, saving the results and IDs as a new set. +updated workflow, saving the results and IDs as a new CSV. ~~~ shell groundtruth submit \ @@ -99,33 +130,31 @@ groundtruth submit \ groundtruth retrieve \ --host try.indico.io --token indico_api_token.txt \ --submission-ids-file remediated_submission_ids.csv \ - --results-folder remediated_results + --results-folder remediated_reviews ~~~ ~~~ shell groundtruth extract \ - --results-folder remediated_results \ - --extractions-file remediated_extractions.csv \ - --model "Invoice Extraction Model" + --results-folder remediated_reviews \ + --samples-file remediations.csv ~~~ -Note that the results and extractions will *not* contain ground truths, only remediated -predictions. Use the `combine` command to combine the ground truths from the original -round of analysis with the remediated predictions from this round. Ground truths and -predictions will be matched up by document file name and field. +Use the `combine` command to combine the ground truths from the original round of +analysis with the remediated predictions from this round. Ground truths and predictions +will be matched up by document filename and field. ~~~ shell groundtruth combine \ - --ground-truths-file ground_truth_extractions.csv \ - --predictions-file remediated_extractions.csv \ - --extractions-file combined_extractions.csv + --ground-truths-file samples.csv \ + --predictions-file remediations.csv \ + --combined-file remediated_samples.csv ~~~ -Use the `analyze` command on the combined extractions CSV to calculate the remediated +Use the `analyze` command on the remediated samples file to calculate the remediated performance metrics. This process can be repeated for as many rounds of remediation as necessary. Additional ground truth documents can be added to the set by submitting, reviewing, -retrieving, and extracting them using a separate submission IDs CSV and extractions -CSV. Afterwards, the submission IDs and extractions for the new documents can be merged -into the original CSVs. +retrieving, and extracting them using a separate submission IDs CSV and samples +file. Afterwards, the submission IDs and samples for the new documents can be merged +into the original samples file. From 5aac9dd3acfcaa7f2bd701deb447d6d35807cd45 Mon Sep 17 00:00:00 2001 From: Michael Welborn Date: Fri, 21 Nov 2025 14:03:57 -0600 Subject: [PATCH 5/8] Sort bundled files to stabilize across multiple runs --- groundtruth/workflows.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/groundtruth/workflows.py b/groundtruth/workflows.py index 9203519..66d025b 100644 --- a/groundtruth/workflows.py +++ b/groundtruth/workflows.py @@ -34,7 +34,7 @@ def submit_documents( # type: ignore[no-any-unimported] yield submission_id elif document_file.is_dir(): - bundle_files = list( + bundle_files = sorted( filter( lambda file: file.is_file() and not file.name.startswith("."), document_file.glob("*"), From 5d1166b3c7850ddc2ad234a177484b872cbb2084 Mon Sep 17 00:00:00 2001 From: Michael Welborn Date: Fri, 21 Nov 2025 14:04:12 -0600 Subject: [PATCH 6/8] Warn and skip failed submissions --- groundtruth/workflows.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/groundtruth/workflows.py b/groundtruth/workflows.py index 66d025b..ddf876a 100644 --- a/groundtruth/workflows.py +++ b/groundtruth/workflows.py @@ -72,6 +72,15 @@ def retrieve_results( # type: ignore[no-any-unimported] ) continue + if submission.status == "FAILED": + rich.print( + "[yellow]" + f"Submission {submission_id} {file_name!r} failed. " + "Skipping." + "[/]" + ) + continue + result = client.call(RetrieveStorageObject(submission.result_file)) sanitized_file_name = sanitize(file_name) From 57c164af934043923e202a10d218fa8853e7628d Mon Sep 17 00:00:00 2001 From: Michael Welborn Date: Fri, 21 Nov 2025 14:04:42 -0600 Subject: [PATCH 7/8] Add command to retry failed submissions --- groundtruth/cli.py | 27 +++++++++++++++++++++++++++ groundtruth/workflows.py | 17 +++++++++++++++++ 2 files changed, 44 insertions(+) diff --git a/groundtruth/cli.py b/groundtruth/cli.py index e3376de..6cecd1b 100644 --- a/groundtruth/cli.py +++ b/groundtruth/cli.py @@ -48,6 +48,33 @@ def submit( ).write_csv(submission_ids_file) +@arguably.command +def retry( + *, + host: Annotated[str, required], + token: Annotated[Path, required], + submission_ids_file: Path = Path("submission_ids.csv"), +) -> None: + import polars + import rich.progress + + from . import workflows + + config = IndicoConfig(host=host, api_token_path=token) + + csv = polars.read_csv(submission_ids_file) + submission_ids = csv["submission_id"] + tracked_submissions = rich.progress.track( + submission_ids, + description="Retrying...", + auto_refresh=False, + ) + workflows.retry_failed_submissions( + config=config, + submission_ids=tracked_submissions, + ) + + @arguably.command def retrieve( *, diff --git a/groundtruth/workflows.py b/groundtruth/workflows.py index ddf876a..6eca42d 100644 --- a/groundtruth/workflows.py +++ b/groundtruth/workflows.py @@ -8,6 +8,7 @@ from indico.queries import ( GetSubmission, RetrieveStorageObject, + RetrySubmission, WorkflowSubmission, ) @@ -87,3 +88,19 @@ def retrieve_results( # type: ignore[no-any-unimported] result_file = Path(sanitized_file_name + ".json") result_file = results_folder / result_file result_file.write_text(json.dumps(result)) + + +def retry_failed_submissions( # type: ignore[no-any-unimported] + config: IndicoConfig, + submission_ids: Iterable[int], +) -> None: + """ + Retry failed submissions. + """ + client = IndicoClient(config) + + for submission_id in submission_ids: + submission = client.call(GetSubmission(submission_id)) + + if submission.status == "FAILED": + client.call(RetrySubmission([submission_id])) From f40874d15d9fdcbaacd7b2b9ddbe94a4a67c3c80 Mon Sep 17 00:00:00 2001 From: Michael Welborn Date: Fri, 21 Nov 2025 14:05:12 -0600 Subject: [PATCH 8/8] Bump version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 4c5306c..9ff4ca8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -11,7 +11,7 @@ authors = [ ] readme = "README.md" requires-python = ">=3.10,<4" -version = "1.3.0" +version = "2.0.0" dependencies = [ "aiometer (>=1.0.0,<2.0.0)", "arguably (>=1.3.0,<2.0.0)",