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Add python -m to asreview commands #52

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Nov 30, 2023
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Add python -m to asreview commands #52

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12 changes: 6 additions & 6 deletions asreviewcontrib/makita/templates/template_arfi.txt.template
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Original file line number Diff line number Diff line change
Expand Up @@ -35,20 +35,20 @@ mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics

# Collect descriptives about the dataset
mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives
asreview data describe {{ dataset.input_file }} -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives/data_stats_{{ dataset.input_file_stem }}.json
python -m asreview data describe {{ dataset.input_file }} -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives/data_stats_{{ dataset.input_file_stem }}.json
{% if create_wordclouds %}

# Generate wordcloud visualizations of all datasets
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_{{ dataset.input_file_stem }}.png --width 800 --height 500
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_relevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --relevant
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_irrelevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --irrelevant
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_{{ dataset.input_file_stem }}.png --width 800 --height 500
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_relevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --relevant
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_irrelevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --irrelevant
{% endif %}

# Simulate runs, collect metrics and create plots
mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files
{% for prior in dataset.priors %}
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 }}
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 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
{% endfor %}

# Generate plot and tables for dataset
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12 changes: 6 additions & 6 deletions asreviewcontrib/makita/templates/template_basic.txt.template
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Original file line number Diff line number Diff line change
Expand Up @@ -37,20 +37,20 @@ mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics

# Collect descriptives about the dataset {{ dataset.input_file_stem }}
mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives
asreview data describe {{ dataset.input_file }} -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives/data_stats_{{ dataset.input_file_stem }}.json
python -m asreview data describe {{ dataset.input_file }} -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives/data_stats_{{ dataset.input_file_stem }}.json
{% if create_wordclouds %}

# Generate wordcloud visualizations of all datasets
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_{{ dataset.input_file_stem }}.png --width 800 --height 500
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_relevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --relevant
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_irrelevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --irrelevant
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_{{ dataset.input_file_stem }}.png --width 800 --height 500
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_relevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --relevant
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_irrelevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --irrelevant
{% endif %}

# Simulate runs
mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files
{% for run in range(dataset.n_runs) %}
asreview simulate {{ dataset.input_file }} -s {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ run }}.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 }}
asreview metrics {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ run }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}_{{ run }}.json
python -m asreview simulate {{ dataset.input_file }} -s {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ run }}.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 }}_{{ run }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}_{{ run }}.json
{% endfor %}

# Generate plot and tables for dataset
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12 changes: 6 additions & 6 deletions asreviewcontrib/makita/templates/template_multiple_models.txt.template
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Original file line number Diff line number Diff line change
Expand Up @@ -34,13 +34,13 @@ mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics

# Collect descriptives about the dataset {{ dataset.input_file_stem }}
mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives
asreview data describe {{ dataset.input_file }} -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives/data_stats_{{ dataset.input_file_stem }}.json
python -m asreview data describe {{ dataset.input_file }} -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/descriptives/data_stats_{{ dataset.input_file_stem }}.json
{% if create_wordclouds %}

# Generate wordcloud visualizations of all datasets
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_{{ dataset.input_file_stem }}.png --width 800 --height 500
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_relevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --relevant
asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_irrelevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --irrelevant
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_{{ dataset.input_file_stem }}.png --width 800 --height 500
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_relevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --relevant
python -m asreview wordcloud {{ dataset.input_file }} -o {{ output_folder }}/figures/wordcloud_irrelevant_{{ dataset.input_file_stem }}.png --width 800 --height 500 --irrelevant
{% endif %}

# Simulate runs
Expand All @@ -53,8 +53,8 @@ mkdir {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files
# Skipped {{ classifier }} + {{ feature_extraction }} model
{% else %}# Classifier = {{ classifier }}, Feature extractor = {{ feature_extraction }} , Query strategy = max
{% for run in range(n_runs) %}
asreview simulate {{ dataset.input_file }} -s {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ run }}.asreview --model {{ classifier }} --query_strategy max --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 }}
asreview metrics {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/state_files/sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ run }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ run }}.json
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 }}_{{ run }}.asreview --model {{ classifier }} --query_strategy max --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 }}_{{ run }}.asreview -o {{ output_folder }}/simulation/{{ dataset.input_file_stem }}/metrics/metrics_sim_{{ dataset.input_file_stem }}_{{ classifier }}_{{ feature_extraction }}_{{ run }}.json
{% endfor %}{% endif %}
{% endfor %}
{% endfor %}
Expand Down