[DOC] Add JOSS badges (#815)

* Add JOSS badges. * Trigger new build. * Update README.md * Add citation to README and index.rst. * Add duecredit citation. * Add reference to workflow docstrings. * Add citation to the report as well. * Add numbers back in.
ME-ICA · Oct 25, 2021 · 28a0c46 · 28a0c46
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -14,7 +14,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Generate environment
           command: |
@@ -24,7 +24,7 @@ jobs:
               pip install .[tests]
             fi
       - save_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
           paths:
               - /opt/conda/envs/tedana_py37
 
@@ -35,7 +35,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py36-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py36-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Generate environment
           command: |
@@ -54,7 +54,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py36
       - save_cache:
-          key: conda-py36-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py36-v2-{{ checksum "tedana/info.py" }}
           paths:
               - /opt/conda/envs/tedana_py36
       - persist_to_workspace:
@@ -69,7 +69,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Running unit tests
           command: |
@@ -91,7 +91,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py38-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py38-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Generate environment
           command: |
@@ -110,7 +110,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py38
       - save_cache:
-          key: conda-py38-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py38-v2-{{ checksum "tedana/info.py" }}
           paths:
               - /opt/conda/envs/tedana_py38
       - persist_to_workspace:
@@ -125,7 +125,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py39-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py39-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Generate environment
           command: |
@@ -144,7 +144,7 @@ jobs:
             mkdir /tmp/src/coverage
             mv /tmp/src/tedana/.coverage /tmp/src/coverage/.coverage.py39
       - save_cache:
-          key: conda-py39-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py39-v2-{{ checksum "tedana/info.py" }}
           paths:
               - /opt/conda/envs/tedana_py39
       - persist_to_workspace:
@@ -159,7 +159,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Style check
           command: |
@@ -175,7 +175,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -200,7 +200,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -225,7 +225,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -250,7 +250,7 @@ jobs:
     steps:
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Run integration tests
           no_output_timeout: 40m
@@ -277,7 +277,7 @@ jobs:
           at: /tmp
       - checkout
       - restore_cache:
-          key: conda-py37-v1-{{ checksum "tedana/info.py" }}
+          key: conda-py37-v2-{{ checksum "tedana/info.py" }}
       - run:
           name: Merge coverage files
           command: |

diff --git a/README.md b/README.md
@@ -2,7 +2,8 @@
 
 [![Latest Version](https://img.shields.io/pypi/v/tedana.svg)](https://pypi.python.org/pypi/tedana/)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/tedana.svg)](https://pypi.python.org/pypi/tedana/)
-[![DOI](https://zenodo.org/badge/110845855.svg)](https://zenodo.org/badge/latestdoi/110845855)
+[![JOSS DOI](https://joss.theoj.org/papers/10.21105/joss.03669/status.svg)](https://doi.org/10.21105/joss.03669)
+[![Zenodo DOI](https://zenodo.org/badge/110845855.svg)](https://zenodo.org/badge/latestdoi/110845855)
 [![License](https://img.shields.io/badge/License-LGPL%202.0-blue.svg)](https://opensource.org/licenses/LGPL-2.1)
 [![CircleCI](https://circleci.com/gh/ME-ICA/tedana.svg?style=shield)](https://circleci.com/gh/ME-ICA/tedana)
 [![Documentation Status](https://readthedocs.org/projects/tedana/badge/?version=latest)](http://tedana.readthedocs.io/en/latest/?badge=latest)
@@ -23,6 +24,26 @@ An important distinction is that while the ME-ICA pipeline originally performed
 
 More information and documentation can be found at https://tedana.readthedocs.io.
 
+## Citing `tedana`
+
+If you use `tedana`, please cite the following papers, as well as our [most recent Zenodo release](https://zenodo.org/badge/latestdoi/110845855):
+
+- DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L.,
+  Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S.,
+  Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S.,
+  Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M.,
+  Whitaker, K., & Handwerker, D. A. (2021).
+  [TE-dependent analysis of multi-echo fMRI with tedana.](https://doi.org/10.21105/joss.03669)
+  _Journal of Open Source Software_, _6(66)_, 3669.
+  doi:10.21105/joss.03669.
+- Kundu, P., Inati, S. J., Evans, J. W., Luh, W. M., & Bandettini, P. A. (2011).
+  [Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI.](https://doi.org/10.1016/j.neuroimage.2011.12.028)
+  _NeuroImage_, _60_, 1759-1770.
+- Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J.,
+  Saad, Z. S., Bandettini, P. A., & Bullmore, E. T. (2013).
+  [Integrated strategy for improving functional connectivity mapping using multiecho fMRI.](https://doi.org/10.1073/pnas.1301725110)
+  _Proceedings of the National Academy of Sciences_, _110_, 16187-16192.
+
 ## Installation
 
 ### Use `tedana` with your local Python environment

diff --git a/docs/index.rst b/docs/index.rst
@@ -12,9 +12,13 @@ tedana: TE Dependent ANAlysis
    :target: https://pypi.python.org/pypi/tedana/
    :alt: PyPI - Python Version
 
+.. image:: https://joss.theoj.org/papers/10.21105/joss.03669/status.svg
+   :target: https://doi.org/10.21105/joss.03669
+   :alt: JOSS DOI
+
 .. image:: https://zenodo.org/badge/110845855.svg
    :target: https://zenodo.org/badge/latestdoi/110845855
-   :alt: DOI
+   :alt: Zenodo DOI
 
 .. image:: https://circleci.com/gh/ME-ICA/tedana.svg?style=shield
    :target: https://circleci.com/gh/ME-ICA/tedana
@@ -110,14 +114,27 @@ When using tedana, please include the following citations:
       <p>
       <span id="tedana_citation">tedana</span> Available from: <a id="tedana_doi_url" href="https://doi.org/10.5281/zenodo.1250561">https://doi.org/10.5281/zenodo.1250561</a>
       <img src onerror='fillCitation()' alt=""/>
+      </p>
+
+      <p>
+      2. DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L.,
+      Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S.,
+      Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S.,
+      Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M.,
+      Whitaker, K., & Handwerker, D. A. (2021).
+      <a href=https://doi.org/10.21105/joss.03669>TE-dependent analysis of multi-echo fMRI with tedana.</a>
+      <i>Journal of Open Source Software</i>, <i>6(66)</i>, 3669.
+      doi:10.21105/joss.03669.
+      </p>
 
       <p>
-      1. Kundu, P., Inati, S. J., Evans, J. W., Luh, W. M. & Bandettini, P. A. (2011).
+      3. Kundu, P., Inati, S. J., Evans, J. W., Luh, W. M., & Bandettini, P. A. (2011).
       <a href=https://doi.org/10.1016/j.neuroimage.2011.12.028>Differentiating BOLD and non-BOLD signals in fMRI time series using multi-echo EPI.</a>
       <i>NeuroImage</i>, <i>60</i>, 1759-1770.
       </p>
+
       <p>
-      1. Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J.,
+      4. Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., Vértes, P. E., Inati, S. J.,
       Saad, Z. S., Bandettini, P. A., & Bullmore, E. T. (2013).
       <a href=https://doi.org/10.1073/pnas.1301725110>Integrated strategy for improving functional connectivity mapping using multiecho fMRI.</a>
       <i>Proceedings of the National Academy of Sciences</i>, <i>110</i>, 16187-16192.

diff --git a/tedana/__init__.py b/tedana/__init__.py
@@ -7,7 +7,7 @@
 
 import warnings
 
-from .due import Doi, due
+from .due import BibTeX, Doi, due
 from .info import (
     __author__,
     __copyright__,
@@ -24,6 +24,14 @@
 # cmp is not used, so ignore nipype-generated warnings
 warnings.filterwarnings("ignore", r"cmp not installed")
 
+# Citation for the package JOSS paper.
+due.cite(
+    Doi("10.21105/joss.03669"),
+    description="Publication introducing tedana.",
+    path="tedana",
+    cite_module=True,
+)
+
 # Citation for the algorithm.
 due.cite(
     Doi("10.1016/j.neuroimage.2011.12.028"),

diff --git a/tedana/workflows/t2smap.py b/tedana/workflows/t2smap.py
@@ -161,6 +161,8 @@ def t2smap_workflow(
     """
     Estimate T2 and S0, and optimally combine data across TEs.
 
+    Please remember to cite [1]_.
+
     Parameters
     ----------
     data : :obj:`str` or :obj:`list` of :obj:`str`
@@ -219,6 +221,16 @@ def t2smap_workflow(
                                   will have a NaN.
     desc-optcom_bold.nii.gz       Optimally combined timeseries.
     ============================= =================================================
+
+    References
+    ----------
+    .. [1] DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L.,
+           Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S.,
+           Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S.,
+           Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M.,
+           Whitaker, K., & Handwerker, D. A. (2021).
+           TE-dependent analysis of multi-echo fMRI with tedana.
+           Journal of Open Source Software, 6(66), 3669. doi:10.21105/joss.03669.
     """
     out_dir = op.abspath(out_dir)
     if not op.isdir(out_dir):

diff --git a/tedana/workflows/tedana.py b/tedana/workflows/tedana.py
@@ -344,6 +344,8 @@ def tedana_workflow(
     """
     Run the "canonical" TE-Dependent ANAlysis workflow.
 
+    Please remember to cite [1]_.
+
     Parameters
     ----------
     data : :obj:`str` or :obj:`list` of :obj:`str`
@@ -426,6 +428,16 @@ def tedana_workflow(
     This workflow writes out several files. For a complete list of the files
     generated by this workflow, please visit
     https://tedana.readthedocs.io/en/latest/outputs.html
+
+    References
+    ----------
+    .. [1] DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L.,
+           Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S.,
+           Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S.,
+           Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M.,
+           Whitaker, K., & Handwerker, D. A. (2021).
+           TE-dependent analysis of multi-echo fMRI with tedana.
+           Journal of Open Source Software, 6(66), 3669. doi:10.21105/joss.03669.
     """
     out_dir = op.abspath(out_dir)
     if not op.isdir(out_dir):
@@ -530,7 +542,20 @@ def tedana_workflow(
     elif t2smap is not None:
         raise IOError("Argument 't2smap' must be an existing file.")
 
-    RepLGR.info("TE-dependence analysis was performed on input data.")
+    RepLGR.info(
+        "TE-dependence analysis was performed on input data using the tedana workflow "
+        "(DuPre, Salo et al., 2021)."
+    )
+    RefLGR.info(
+        "DuPre, E. M., Salo, T., Ahmed, Z., Bandettini, P. A., Bottenhorn, K. L., "
+        "Caballero-Gaudes, C., Dowdle, L. T., Gonzalez-Castillo, J., Heunis, S., "
+        "Kundu, P., Laird, A. R., Markello, R., Markiewicz, C. J., Moia, S., "
+        "Staden, I., Teves, J. B., Uruñuela, E., Vaziri-Pashkam, M., "
+        "Whitaker, K., & Handwerker, D. A. (2021). "
+        "TE-dependent analysis of multi-echo fMRI with tedana. "
+        "Journal of Open Source Software, 6(66), 3669. doi:10.21105/joss.03669."
+    )
+
     if mask and not t2smap:
         # TODO: add affine check
         LGR.info("Using user-defined mask")