From 8351d16e51f5e7bc5102f44af4e4b233e53550ff Mon Sep 17 00:00:00 2001 From: Jelle Teijema Date: Mon, 3 Feb 2025 14:32:54 +0100 Subject: [PATCH] Add --quiet tag to metrics (#83) Co-authored-by: Jelle --- README.md | 8 ++++++++ asreviewcontrib/makita/templates/doc_README.md.template | 2 +- .../makita/templates/template_arfi.txt.template | 2 +- .../makita/templates/template_basic.txt.template | 2 +- .../makita/templates/template_multimodel.txt.template | 2 +- .../makita/templates/template_prior.txt.template | 4 ++-- 6 files changed, 14 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index ad9c147..b426588 100644 --- a/README.md +++ b/README.md @@ -47,6 +47,14 @@ Requires Python 3.8 or higher. pip install asreview-makita ``` +This project requires additional Python packages. You can install them using the following command: + +```bash +pip install asreview-datatools asreview-insights +``` + +Alternatively, check the README.md file in your Makita project folder for specific dependencies. + ### For upgrading, use: ```bash diff --git a/asreviewcontrib/makita/templates/doc_README.md.template b/asreviewcontrib/makita/templates/doc_README.md.template index cd74724..eaacc93 100644 --- a/asreviewcontrib/makita/templates/doc_README.md.template +++ b/asreviewcontrib/makita/templates/doc_README.md.template @@ -11,7 +11,7 @@ The template is described as: '{{ template_name_long }}'. This project depends on Python 3.7 or later (python.org/download), and [ASReview](https://asreview.nl/download/). Install the following dependencies to run the simulation and analysis in this project. ```sh -pip install asreview>=1.0 asreview-insights>=1.3 asreview-datatools +pip install asreview>=1.0 asreview-insights>=1.5 asreview-datatools ``` {% if not skip_wordclouds %} For generating wordclouds, install the following dependencies. diff --git a/asreviewcontrib/makita/templates/template_arfi.txt.template b/asreviewcontrib/makita/templates/template_arfi.txt.template index 99a7bea..65118de 100644 --- a/asreviewcontrib/makita/templates/template_arfi.txt.template +++ b/asreviewcontrib/makita/templates/template_arfi.txt.template @@ -48,7 +48,7 @@ python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/fig mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files {% for prior in dataset.priors %} python -m asreview simulate {{ dataset.input_file }} -s {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ prior[0] }}.asreview --prior_record_id {{ " ".join(prior) }} --seed {{ dataset.model_seed }} -m {{ classifier }} -e {{ feature_extractor }} -q {{ query_strategy }} -b {{ balance_strategy }} --n_instances {{ instances_per_query }} --stop_if {{ stop_if }} -python -m asreview metrics {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ prior[0] }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}_{{ prior[0] }}.json +python -m asreview metrics {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ prior[0] }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}_{{ prior[0] }}.json --quiet {% endfor %} # Generate plot and tables for dataset diff --git a/asreviewcontrib/makita/templates/template_basic.txt.template b/asreviewcontrib/makita/templates/template_basic.txt.template index 734e072..db84c8f 100644 --- a/asreviewcontrib/makita/templates/template_basic.txt.template +++ b/asreviewcontrib/makita/templates/template_basic.txt.template @@ -50,7 +50,7 @@ python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/fig mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files {% for run in range(n_runs) %} python -m asreview simulate {{ dataset.input_file }} -s {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview --init_seed {{ dataset.init_seed + run }} --seed {{ dataset.model_seed + run }} -m {{ classifier }} -e {{ feature_extractor }} -q {{ query_strategy }} -b {{ balance_strategy }} --n_instances {{ instances_per_query }} --stop_if {{ stop_if }} -python -m asreview metrics {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}{{ "_{}".format(run) if n_runs > 1 else "" }}.json +python -m asreview metrics {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}{{ "_{}".format(run) if n_runs > 1 else "" }}.json --quiet {% endfor %} # Generate plot and tables for dataset diff --git a/asreviewcontrib/makita/templates/template_multimodel.txt.template b/asreviewcontrib/makita/templates/template_multimodel.txt.template index f0b8a94..0330744 100644 --- a/asreviewcontrib/makita/templates/template_multimodel.txt.template +++ b/asreviewcontrib/makita/templates/template_multimodel.txt.template @@ -56,7 +56,7 @@ mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files {% else %}# Classifier = {{ classifier }}, Feature extractor = {{ feature_extraction }}, Query strategy = {{ query_strategy }}, Balance strategy = {{balance_strategy}} {% for run in range(n_runs) %} python -m asreview simulate {{ dataset.input_file }} -s {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ query_strategy }}_{{ balance_strategy }}{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview --model {{ classifier }} --query_strategy {{query_strategy}} --feature_extraction {{ feature_extraction }} --init_seed {{ dataset.init_seed + run }} --seed {{ dataset.model_seed }} -q {{ query_strategy }} -b {{ balance_strategy }} --n_instances {{ instances_per_query }} --stop_if {{ stop_if }} -python -m asreview metrics {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ query_strategy }}_{{ balance_strategy }}{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ query_strategy }}_{{ balance_strategy }}{{ "_{}".format(run) if n_runs > 1 else "" }}.json +python -m asreview metrics {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ query_strategy }}_{{ balance_strategy }}{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ query_strategy }}_{{ balance_strategy }}{{ "_{}".format(run) if n_runs > 1 else "" }}.json --quiet {% endfor %}{% endif %} {% endfor %} {% endfor %} diff --git a/asreviewcontrib/makita/templates/template_prior.txt.template b/asreviewcontrib/makita/templates/template_prior.txt.template index c295f28..b17ed38 100644 --- a/asreviewcontrib/makita/templates/template_prior.txt.template +++ b/asreviewcontrib/makita/templates/template_prior.txt.template @@ -40,10 +40,10 @@ python -m asreview wordcloud {{ filepath_without_priors }} -o {{ output_folder } {% for run in range(n_runs) %} python -m asreview simulate {{ filepath_with_priors }} -s {{ output_folder }}/simulation/state_files/sim_custom_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview --seed {{ model_seed + run }} -m {{ classifier }} -e {{ feature_extractor }} -q {{ query_strategy }} -b {{ balance_strategy }} --n_instances {{ instances_per_query }} --stop_if {{ stop_if }} --prior_idx {{ prior_idx }} -python -m asreview metrics {{ output_folder }}/simulation/state_files/sim_custom_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview -o {{ output_folder }}/simulation/metrics/metrics_sim_custom_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.json +python -m asreview metrics {{ output_folder }}/simulation/state_files/sim_custom_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview -o {{ output_folder }}/simulation/metrics/metrics_sim_custom_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.json --quiet python -m asreview simulate {{ filepath_without_priors }} -s {{ output_folder }}/simulation/state_files/sim_minimal_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview --init_seed {{ init_seed + run }} --seed {{ model_seed + run }} -m {{ classifier }} -e {{ feature_extractor }} -q {{ query_strategy }} -b {{ balance_strategy }} --n_instances {{ instances_per_query }} --stop_if {{ stop_if }} -python -m asreview metrics {{ output_folder }}/simulation/state_files/sim_minimal_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview -o {{ output_folder }}/simulation/metrics/metrics_sim_minimal_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.json +python -m asreview metrics {{ output_folder }}/simulation/state_files/sim_minimal_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.asreview -o {{ output_folder }}/simulation/metrics/metrics_sim_minimal_priors{{ "_{}".format(run) if n_runs > 1 else "" }}.json --quiet {% endfor %} # Generate plot and tables for dataset