From bf7303d85f93347eed2f99b80f9bc971d979cf79 Mon Sep 17 00:00:00 2001 From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com> Date: Thu, 9 Jul 2026 20:24:12 +0200 Subject: [PATCH 1/7] Miguel comments --- .github/workflows/autoformat.yml | 13 ++++++++++++- CITATION.cff | 24 ++++++++++++++++++++++++ README.md | 2 +- pyproject.toml | 4 ++-- 4 files changed, 39 insertions(+), 4 deletions(-) create mode 100644 CITATION.cff diff --git a/.github/workflows/autoformat.yml b/.github/workflows/autoformat.yml index 2ba0f94..c194a09 100644 --- a/.github/workflows/autoformat.yml +++ b/.github/workflows/autoformat.yml @@ -26,7 +26,18 @@ jobs: - name: Sort imports with isort run: isort . - + + - name: Sync version into CITATION.cff + run: | + python - <<'EOF' + import pathlib, re, tomllib + version = tomllib.load(open("pyproject.toml", "rb"))["project"]["version"] + cff = pathlib.Path("CITATION.cff") + text = re.sub(r"^version:.*$", f"version: {version}", cff.read_text(), flags=re.M) + cff.write_text(text) + print(f"Synced CITATION.cff to version {version}") + EOF + - name: Commit changes run: | git config --local user.email "github-actions[bot]@users.noreply.github.com" diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..8b5d3b3 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,24 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it using the following metadata." +authors: + - family-name O'Dea + given-name: Ryan + affiliation: CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health + orcid: https://orcid.org/0009-0000-0103-9546 + - family-name: Palmer + given-name: Tom + affiliation: MRC Integrative Epidemiology Unit, University of Bristol + orcid: https://orcid.org/0000-0003-4655-4511 + - family-name: Szmulewicz + given-name: Alejandro + affiliation: CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health + affiliation: McLean Hospital + affiliation: Department of Psychiatry, Harvard Medical School + orcid: https://orcid.org/0000-0002-2664-802X + - family-name: Hernán + given-name: Miguel A. + affiliation: CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health + affiliation: Department of Biostatistics, Harvard T.H. Chan School of Public Health + orcid: https://orcid.org/0000-0003-1619-8456 +title: "pySEQTarget: Sequential Target Trial Emulation" +version: 0.14.0 \ No newline at end of file diff --git a/README.md b/README.md index 6329603..a7d42e4 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# pySEQTarget - Sequentially Nested Target Trial Emulation +# pySEQTarget - Sequential Target Trial Emulation [![PyPI version](https://badge.fury.io/py/pySEQTarget.svg)](https://pypi.org/project/pySEQTarget) [![Downloads](https://static.pepy.tech/badge/pySEQTarget)](https://pepy.tech/project/pySEQTarget) [![codecov](https://codecov.io/gh/CausalInference/pySEQTarget/graph/badge.svg?token=DMOVJJUWXP)](https://codecov.io/gh/CausalInference/pySEQTarget)[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT) diff --git a/pyproject.toml b/pyproject.toml index d463f86..4a3be99 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta" [project] name = "pySEQTarget" version = "0.14.0" -description = "Sequentially Nested Target Trial Emulation" +description = "Sequential Target Trial Emulation" readme = "README.md" license = {text = "MIT"} keywords = ["causal inference", "sequential trial emulation", "target trial", "observational studies"] @@ -23,8 +23,8 @@ classifiers = [ authors = [ {name = "Ryan O'Dea", email = "ryan.odea@psi.ch"}, - {name = "Alejandro Szmulewicz", email = "aszmulewicz@hsph.harvard.edu"}, {name = "Tom Palmer", email = "remlapmot@hotmail.com"}, + {name = "Alejandro Szmulewicz", email = "aszmulewicz@hsph.harvard.edu"}, {name = "Miguel Hernán", email = "mhernan@hsph.harvard.edu"}, ] From 080f193a90191d2d623ccb4ce6fc4c7f500969f0 Mon Sep 17 00:00:00 2001 From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com> Date: Thu, 9 Jul 2026 20:32:53 +0200 Subject: [PATCH 2/7] fix malformed field --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 8b5d3b3..a997fec 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,7 +1,7 @@ cff-version: 1.2.0 message: "If you use this software, please cite it using the following metadata." authors: - - family-name O'Dea + - family-name: O'Dea given-name: Ryan affiliation: CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health orcid: https://orcid.org/0009-0000-0103-9546 From 6607cec024378b004a25fe828a27cca3b2d1a30c Mon Sep 17 00:00:00 2001 From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com> Date: Thu, 9 Jul 2026 20:41:12 +0200 Subject: [PATCH 3/7] bulk search for 'sequentially' --- pySEQTarget/SEQuential.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pySEQTarget/SEQuential.py b/pySEQTarget/SEQuential.py index d979e67..c120b93 100644 --- a/pySEQTarget/SEQuential.py +++ b/pySEQTarget/SEQuential.py @@ -30,7 +30,7 @@ class SEQuential: """ - Primary class initializer for SEQuentially nested target trial emulation + Primary class initializer for SEQuential target trial emulation :param data: Data for analysis :param id_col: Column name for unique patient IDs @@ -126,7 +126,7 @@ def __getstate__(self): def expand(self): """ - Creates the sequentially nested, emulated target trial structure. + Creates the sequential, emulated target trial structure. If ``expand_only`` is set in parameters, returns the expanded dataset as a :class:`polars.DataFrame` and skips all subsequent analysis steps. """ From 188c7d60ad6e35ed6fe334724deef279fc8e65fb Mon Sep 17 00:00:00 2001 From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com> Date: Fri, 10 Jul 2026 09:57:36 +0200 Subject: [PATCH 4/7] Update CITATION.cff Co-authored-by: Tom Palmer --- CITATION.cff | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index a997fec..d8d9895 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -17,8 +17,7 @@ authors: orcid: https://orcid.org/0000-0002-2664-802X - family-name: Hernán given-name: Miguel A. - affiliation: CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health - affiliation: Department of Biostatistics, Harvard T.H. Chan School of Public Health + affiliation: "CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health; Department of Biostatistics, Harvard T.H. Chan School of Public Health" orcid: https://orcid.org/0000-0003-1619-8456 title: "pySEQTarget: Sequential Target Trial Emulation" version: 0.14.0 \ No newline at end of file From 4148bcd8b804483abcd3e6ab597da09803a3e27e Mon Sep 17 00:00:00 2001 From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com> Date: Fri, 10 Jul 2026 09:57:51 +0200 Subject: [PATCH 5/7] Update CITATION.cff Co-authored-by: Tom Palmer --- CITATION.cff | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index d8d9895..8f1499c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -20,4 +20,7 @@ authors: affiliation: "CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health; Department of Biostatistics, Harvard T.H. Chan School of Public Health" orcid: https://orcid.org/0000-0003-1619-8456 title: "pySEQTarget: Sequential Target Trial Emulation" -version: 0.14.0 \ No newline at end of file +version: 0.14.0 +url: https://pyseqtarget.readthedocs.io/ +repository-code: https://github.com/CausalInference/pySEQTarget +repository-artifact: https://pypi.org/project/pySEQTarget/ \ No newline at end of file From 497851f4e6c7825b12e46c0228bd8dca40ff4051 Mon Sep 17 00:00:00 2001 From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com> Date: Fri, 10 Jul 2026 09:58:03 +0200 Subject: [PATCH 6/7] Update CITATION.cff Co-authored-by: Tom Palmer --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 8f1499c..93af9ab 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -7,7 +7,7 @@ authors: orcid: https://orcid.org/0009-0000-0103-9546 - family-name: Palmer given-name: Tom - affiliation: MRC Integrative Epidemiology Unit, University of Bristol + affiliation: "MRC Integrative Epidemiology Unit and Population Health Sciences, University of Bristol" orcid: https://orcid.org/0000-0003-4655-4511 - family-name: Szmulewicz given-name: Alejandro From 6e7c3873374111bea331790a3de4b89fc959383e Mon Sep 17 00:00:00 2001 From: Ryan O'Dea <70209371+ryan-odea@users.noreply.github.com> Date: Fri, 10 Jul 2026 09:58:10 +0200 Subject: [PATCH 7/7] Update CITATION.cff Co-authored-by: Tom Palmer --- CITATION.cff | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 93af9ab..6abf4d9 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -11,9 +11,7 @@ authors: orcid: https://orcid.org/0000-0003-4655-4511 - family-name: Szmulewicz given-name: Alejandro - affiliation: CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health - affiliation: McLean Hospital - affiliation: Department of Psychiatry, Harvard Medical School + affiliation: "CAUSALab, Department of Epidemiology, Harvard T.H. Chan School of Public Health; McLean Hospital; Department of Psychiatry, Harvard Medical School" orcid: https://orcid.org/0000-0002-2664-802X - family-name: Hernán given-name: Miguel A.