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richarddushimeLukasWallrichclaude
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Fix FLoRA citation update to support repeated runs (#688)
* Add automated FLoRA citation update from FReD-data - Extend update_fred_citation.py to replace {{flora-ref}} placeholder in content/replication-hub/flora/_index.md with the HTML-formatted citation - Add content/replication-hub/flora/_index.md (source file with placeholder) - Update data-processing workflow to stage and commit the resolved _index.md to the build-resources branch alongside fred_citation.txt The citation update already ran weekly on Sundays; the new _index.md replacement runs on the same schedule with no additional triggers needed. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> * flora citation update --------- Co-authored-by: Lukas Wallrich <lukas.wallrich@gmail.com> Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
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‎content/replication-hub/flora/_index.md‎

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@@ -19,9 +19,12 @@ With this simple structure FLoRA allows for tracking of replication rates across
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In FLoRA, years of work from a large community of volunteers culminate. If you would like to contribute to the project or use the data for your own research, we would strongly appreciate you reaching out to us.
2020

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**How to cite:**
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<!-- flora-citation-start -->
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{{< alert note >}}
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Wallrich, L.*, & Röseler, L.*, Hartmann, H., Ashcroft-Jones, S., Doetsch, C., Kaiser, L., Schüller, S. M., Aldoh, A., Behbood, H., Elsherif, M. M., Klett, N., Krapp, J., Liu, M., Pavlović, Z., Pennington, C. R., Schütz, A., Seida, C., Siziva, K., Skvortsova, A., Aczel, B., Adelina, N., Agostini, V., Al-Hoorie, A. H., Alarie, S., Albayrak-Aydemir, N., Alzahawi, S., Anvari, F., Arriaga, P., Baker, B. J., Barth, C. L., Bauer, D. J., Becker, R., Beitner, J., Belaus, A., Bhatt, H., Bhogal, J., Boyce, V., Breemer, L., Brick, C., Brohmer, H., Brummernhenrich, B., Budd, E., Butler, A., Casula, A., Chandrashekar, S. P., Chen, S., Chung, K. L., Cockcroft, J. P., Crowe, P., Cummins, J., Daniel, A., Deane, O., Deressa, T. K., Dienlin, T., Diveica, V., Draguns, A., Dumbalska, T., Efendic, E., El Halabi, M., Enright, S., Evans, T. R., Exner, A., Farrar, B. G., Feldman, G., Fillon, A., Floyd, J., Fontana Vieira, F., Frese, J., Förster, N., Gattie, M. C., Gemmecke, C., Genschow, O., Giannouli, V., Gjoneska, B., Gnambs, T., Gourdon-Kanhukamwe, A., Graham, C. J., Greshake Tzovaras, B., Guay, S., Hausenloy, J., Haviva, C., Henderson, E. L., Herderich, A., Hilbert, L., Holgado, D., Hussey, I., Höfer, L., Ilchovska, Z. G., Imada, H., Imwene, P., Izydorczak, K., Jaubert, S., Jeftić, A., Kalandadze, T., Kamermans, K., Karhulahti, V., Kasseckert, L., Kastrinogiannis, A., Klingelhöfer-Jens, M., Kocalar, H. E., Koppel, L., Koppold, A., Korbmacher, M., Kujawa, Z., Kulke, L., Kumar, P., Kuper, N., LaPlume, A. A., Lach, R., Lecuona, O., Lee, J., Leech, G., Leksina, E., Lin, C., Liu, Y., Lohkamp, F., Lou, N. M., Lynott, D., Mackinnon, S., Maier, M., Maiya, S., Makel, M. C., Manrique-Castano, D., Manríquez-Robles, D., Mathes, L., McSharry, D., Meidenbauer, K. L., Meier, M., Micheli, L., Miller, T., Montefinese, M., Moreau, D., Moser, N., Mrkva, K., Murphy, J., Muthu, J., Narkar, N., Nemcova, M., Nádvorník, J., O'Mahoney, R., O'Mahony, A., Oberholzer, Y., Oomen, D., Osano, M., Otstavnov, N., Packheiser, J., Pandey, S., Panton, H., Papenmeier, F., Parsons, S., Paruzel-Czachura, M., Pavlov, Y. G., Pittelkow, M., Plomp, W., Plonski, P. E., Pravednikov, A., Pronizius, E., Pua, A., Pypno-Blajda, K., Rausch, M., Raza, H., Reason, R., Rebholz, T. R., Resulbegoviq, H., Richert, E., Ross, R. M., Russo, S., Röer, J. P., Sandkühler, J. F., Schmidt, K., Sempere, N., Sobolak, R., Sperl, M. F., Stevens, J. R., Stogianni, M., Szekely, R., Tan, A. W., Thürmer, J. L., Tiulpakova, M., Tomczak, J., Tołopiło, A., Tunca, B., Vanpaemel, W., Vaughn, L. A., Verheyen, S., Vineyard, G. H., Weber, L., Weinberg, A., Wingen, S., Wolska, J., Yeung, S. K., Younssi, M., Zaneva, M., Zimmermann, D., Azevedo, F. (2026). FORRT Library of Replication Attempts (FLoRA) [Data set]. OSF. <a href="https://doi.org/10.17605/OSF.IO/9R62X">https://doi.org/10.17605/OSF.IO/9R62X</a>
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\* These authors contributed equally to this work.
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<strong>* These authors contributed equally to this work.</strong>
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{{< /alert >}}
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<!-- flora-citation-end -->

‎scripts/update_fred_citation.py‎

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@@ -8,6 +8,7 @@
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And saves it to static/data/fred_citation.txt for use in the cite_us page.
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"""
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import re
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import sys
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import logging
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from pathlib import Path
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CITATION_URL = "https://raw.githubusercontent.com/forrtproject/FReD-data/refs/heads/main/output/citation.txt"
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OUTPUT_FILE = "static/data/fred_citation.txt"
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FLORA_INDEX_FILE = "content/replication-hub/flora/_index.md"
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FLORA_PLACEHOLDER = "{{flora-ref}}"
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def fetch_fred_citation():
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"""
@@ -64,7 +64,6 @@ def save_citation(citation, output_path):
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# Post-process citation to match required format
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# Replace DOI URL with HTML link and append note if not present
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import re
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# Find DOI URL (assume starts with https://doi.org/)
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citation = citation.strip()
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# Remove any trailing note
@@ -80,8 +79,8 @@ def repl(match):
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return f'<a href="{url}">{url}</a>'
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citation_main = re.sub(doi_pattern, repl, citation_main)
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# Compose final citation
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citation_final = citation_main + "\n\n" + note + "\n"
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# Compose final citation with highlighted note
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citation_final = citation_main + "\n\n<strong>" + note + "</strong>\n"
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with open(output_file, 'w', encoding='utf-8') as f:
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f.write(citation_final)
@@ -94,13 +93,16 @@ def repl(match):
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def update_flora_index(citation_html):
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"""
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Replace the {{flora-ref}} placeholder in the FLoRA _index.md with the citation HTML.
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Update the citation inside the flora-citation block in the FLoRA _index.md.
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The function looks for <!-- flora-citation-start --> and <!-- flora-citation-end --> markers,
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and replaces the content between {{< alert note >}} and {{< /alert >}} with the citation.
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Args:
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citation_html: The processed citation HTML string (same as saved to fred_citation.txt)
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citation_html: The processed citation HTML string
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Returns:
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bool: True if successful or placeholder not present, False on error
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bool: True if successful or markers not present, False on error
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"""
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try:
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index_file = Path(FLORA_INDEX_FILE)
@@ -109,13 +111,45 @@ def update_flora_index(citation_html):
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return False
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content = index_file.read_text(encoding='utf-8')
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if FLORA_PLACEHOLDER not in content:
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logger.info("No {{flora-ref}} placeholder found in FLoRA index, skipping")
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start_marker = "<!-- flora-citation-start -->"
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end_marker = "<!-- flora-citation-end -->"
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alert_start = "{{< alert note >}}"
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alert_end = "{{< /alert >}}"
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if start_marker not in content or end_marker not in content:
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logger.info("No flora citation block markers found in FLoRA index, skipping")
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return True
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# Find flora-citation block (escape markers for regex)
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flora_block_pattern = re.compile(
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rf"({re.escape(start_marker)})(.*?){re.escape(end_marker)}",
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re.DOTALL
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)
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flora_block_match = flora_block_pattern.search(content)
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if not flora_block_match:
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logger.info("No flora citation block found, skipping")
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return True
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flora_block = flora_block_match.group(2)
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# Find alert note block inside flora-citation block (escape Hugo shortcode for regex)
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alert_pattern = re.compile(
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rf"({re.escape(alert_start)})(.*?){re.escape(alert_end)}",
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re.DOTALL
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)
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alert_match = alert_pattern.search(flora_block)
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if not alert_match:
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logger.info("No alert note block found inside flora citation block, skipping")
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return True
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updated = content.replace(FLORA_PLACEHOLDER, citation_html.strip())
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# Replace content between alert markers
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new_alert_block = f"{alert_start}\n{citation_html.strip()}\n{alert_end}"
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new_flora_block = alert_pattern.sub(new_alert_block, flora_block)
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# Rebuild flora-citation block
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new_flora_citation = f"{start_marker}\n{new_flora_block}\n{end_marker}"
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# Replace in file (use lambda to avoid backreference issues)
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updated = flora_block_pattern.sub(lambda m: new_flora_citation, content)
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index_file.write_text(updated, encoding='utf-8')
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logger.info(f"Successfully updated {FLORA_INDEX_FILE}")
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logger.info(f"Successfully updated citation inside alert note in {FLORA_INDEX_FILE}")
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return True
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except Exception as e:
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logger.error(f"Failed to update FLoRA index: {e}")
@@ -138,7 +172,6 @@ def main():
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return 1
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# Build the HTML-formatted citation string (same logic as save_citation)
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import re
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citation_stripped = citation.strip()
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note = "* These authors contributed equally to this work."
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citation_main = citation_stripped
@@ -148,7 +181,7 @@ def main():
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def repl(match):
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url = match.group(1)
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return f'<a href="{url}">{url}</a>'
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citation_html = re.sub(doi_pattern, repl, citation_main) + "\n\n" + note
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citation_html = re.sub(doi_pattern, repl, citation_main) + "\n\n<strong>" + note + "</strong>"
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# Replace placeholder in FLoRA _index.md
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if not update_flora_index(citation_html):

‎static/data/fred_citation.txt‎

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@@ -1,3 +1,3 @@
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Wallrich, L.*, & Röseler, L.*, Hartmann, H., Ashcroft-Jones, S., Doetsch, C., Kaiser, L., Schüller, S. M., Aldoh, A., Behbood, H., Elsherif, M. M., Klett, N., Krapp, J., Liu, M., Pavlović, Z., Pennington, C. R., Schütz, A., Seida, C., Siziva, K., Skvortsova, A., Aczel, B., Adelina, N., Agostini, V., Al-Hoorie, A. H., Alarie, S., Albayrak-Aydemir, N., Alzahawi, S., Anvari, F., Arriaga, P., Baker, B. J., Barth, C. L., Bauer, D. J., Becker, R., Beitner, J., Belaus, A., Bhatt, H., Bhogal, J., Boyce, V., Breemer, L., Brick, C., Brohmer, H., Brummernhenrich, B., Budd, E., Butler, A., Casula, A., Chandrashekar, S. P., Chen, S., Chung, K. L., Cockcroft, J. P., Crowe, P., Cummins, J., Daniel, A., Deane, O., Deressa, T. K., Dienlin, T., Diveica, V., Draguns, A., Dumbalska, T., Efendic, E., El Halabi, M., Enright, S., Evans, T. R., Exner, A., Farrar, B. G., Feldman, G., Fillon, A., Floyd, J., Fontana Vieira, F., Frese, J., Förster, N., Gattie, M. C., Gemmecke, C., Genschow, O., Giannouli, V., Gjoneska, B., Gnambs, T., Gourdon-Kanhukamwe, A., Graham, C. J., Greshake Tzovaras, B., Guay, S., Hausenloy, J., Haviva, C., Henderson, E. L., Herderich, A., Hilbert, L., Holgado, D., Hussey, I., Höfer, L., Ilchovska, Z. G., Imada, H., Imwene, P., Izydorczak, K., Jaubert, S., Jeftić, A., Kalandadze, T., Kamermans, K., Karhulahti, V., Kasseckert, L., Kastrinogiannis, A., Klingelhöfer-Jens, M., Kocalar, H. E., Koppel, L., Koppold, A., Korbmacher, M., Kujawa, Z., Kulke, L., Kumar, P., Kuper, N., LaPlume, A. A., Lach, R., Lecuona, O., Lee, J., Leech, G., Leksina, E., Lin, C., Liu, Y., Lohkamp, F., Lou, N. M., Lynott, D., Mackinnon, S., Maier, M., Maiya, S., Makel, M. C., Manrique-Castano, D., Manríquez-Robles, D., Mathes, L., McSharry, D., Meidenbauer, K. L., Meier, M., Micheli, L., Miller, T., Montefinese, M., Moreau, D., Moser, N., Mrkva, K., Murphy, J., Muthu, J., Narkar, N., Nemcova, M., Nádvorník, J., O'Mahoney, R., O'Mahony, A., Oberholzer, Y., Oomen, D., Osano, M., Otstavnov, N., Packheiser, J., Pandey, S., Panton, H., Papenmeier, F., Parsons, S., Paruzel-Czachura, M., Pavlov, Y. G., Pittelkow, M., Plomp, W., Plonski, P. E., Pravednikov, A., Pronizius, E., Pua, A., Pypno-Blajda, K., Rausch, M., Raza, H., Reason, R., Rebholz, T. R., Resulbegoviq, H., Richert, E., Ross, R. M., Russo, S., Röer, J. P., Sandkühler, J. F., Schmidt, K., Sempere, N., Sobolak, R., Sperl, M. F., Stevens, J. R., Stogianni, M., Szekely, R., Tan, A. W., Thürmer, J. L., Tiulpakova, M., Tomczak, J., Tołopiło, A., Tunca, B., Vanpaemel, W., Vaughn, L. A., Verheyen, S., Vineyard, G. H., Weber, L., Weinberg, A., Wingen, S., Wolska, J., Yeung, S. K., Younssi, M., Zaneva, M., Zimmermann, D., Azevedo, F. (2026). FORRT Library of Replication Attempts (FLoRA) [Data set]. OSF. <a href="https://doi.org/10.17605/OSF.IO/9R62X">https://doi.org/10.17605/OSF.IO/9R62X</a>
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* These authors contributed equally to this work.
3+
<strong>* These authors contributed equally to this work.</strong>

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