Repository: FCP-INDI/cpac

Issue:
✨ Call `ba-timeseries-gradients` and `tsconcat` from wrapper
<!-- ### User interface changes

_No response_ -->

### Project sub-parts and estimates

- [x] Call `ba_timeseries_gradients` from `cpac` ① (#42)
- [x] Call `tsconcat` from `cpac` ① (#43)

### Timeline notes

#### version management
* `ba_timeseries_gradients` requires Python ≥ 3.11, < 3.12
* `tsconcat` requires Python ≥ 3.11

<!-- ### Timesink notes

_No response_ -->

### Frustration notes

I think the risk : reward and cost : benefit ratios are too high for these features, even though the risks and costs are low. Adding other scripts to be used directly as-is at the same level of abstraction without any other integration adds opportunity for error (more places for typos, more code and documentation to maintain) without any added value that I can see.

### Design decisions and notes

~~I think I'll add a `--version` flag to each of the newly wrapped commands to specify a version of the wrapped packages, defaulting to the most recent release.~~ (didn't happen)

Discussion:

Patch:
diff --git a/README.rst b/README.rst
index b3ae0590..deb6819a 100644
--- a/README.rst
+++ b/README.rst
@@ -33,7 +33,7 @@ Usage
     usage: cpac [-h] [--version] [-o OPT] [-B CUSTOM_BINDING]
                 [--platform {docker,singularity}] [--image IMAGE] [--tag TAG]
                 [--working_dir PATH] [-v] [-vv]
-                {run,utils,version,group,gradients,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
+                {run,utils,version,group,gradients,tsconcat,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
                 ...
     
     cpac: a Python package that simplifies using C-PAC <http://fcp-indi.github.io> containerized images. 
@@ -68,7 +68,7 @@ Usage
     - https://github.com/FCP-INDI/cpac/issues
     
     positional arguments:
-      {run,utils,version,group,gradients,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
+      {run,utils,version,group,gradients,tsconcat,pull,upgrade,enter,bash,shell,parse-resources,parse_resources,crash}
         run                 Run C-PAC. See
                             "cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] run --help"
                             for more information.
@@ -80,6 +80,7 @@ Usage
                             "cpac [--platform {docker,singularity}] [--image IMAGE] [--tag TAG] group --help"
                             for more information.
         gradients           Run ba_timeseries_gradients
+        tsconcat            Run ba-tsconcat
         pull (upgrade)      Upgrade your local C-PAC version to the latest version
                             by pulling from Docker Hub or other repository.
                             Use with "--image" and/or "--tag" to specify an image
diff --git a/poetry.lock b/poetry.lock
index 8a6a35ed..d4f42b0a 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -22,24 +22,6 @@ files = [
     {file = "astor-0.8.1.tar.gz", hash = "sha256:6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e"},
 ]
 
-[[package]]
-name = "attrs"
-version = "23.1.0"
-description = "Classes Without Boilerplate"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
-    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
-]
-
-[package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-
 [[package]]
 name = "ba-timeseries-gradients"
 version = "0.1.0"
@@ -92,6 +74,26 @@ files = [
     {file = "bids_validator-1.14.0-py3-none-any.whl", hash = "sha256:bab89f97a8d833235562cf0f3ac981bfca71acf2793a6c12a8af631c29ee0b8f"},
 ]
 
+[[package]]
+name = "bids2table"
+version = "0.1.0a0"
+description = "Efficiently index large-scale BIDS datasets and derivatives"
+optional = true
+python-versions = ">=3.8"
+files = [
+    {file = "bids2table-0.1.0a0-py3-none-any.whl", hash = "sha256:2578f0e2b20e35cb3cfb0e9c00032a4d7f348bc20d3275557ca4b5d3d011206e"},
+    {file = "bids2table-0.1.0a0.tar.gz", hash = "sha256:231fe82b061b1125866cc1ada77d4f46788ac380b99eeb157634af694df40309"},
+]
+
+[package.dependencies]
+elbow = "*"
+nibabel = "*"
+pandas = "*"
+
+[package.extras]
+dev = ["black (==23.3.0)", "flake8 (==5.0.4)", "isort (==5.11.5)", "mypy (==1.2.0)", "pdoc (==14.0.0)", "pre-commit", "pylint (>=2.5.0)", "setuptools-scm"]
+test = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "brainspace"
 version = "0.1.10"
@@ -116,41 +118,22 @@ vtk = ">=8.1.0"
 [package.extras]
 test = ["coverage", "coveralls", "matplotlib (>=2.0.0)", "nibabel", "numpy (>=1.11.0)", "pandas", "pillow", "pytest", "pytest-cov", "scikit-learn (>=0.20.0)", "scipy (>=0.17.0)", "vtk (>=8.1.0)"]
 
-[[package]]
-name = "cachecontrol"
-version = "0.12.14"
-description = "httplib2 caching for requests"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "CacheControl-0.12.14-py2.py3-none-any.whl", hash = "sha256:1c2939be362a70c4e5f02c6249462b3b7a24441e4f1ced5e9ef028172edf356a"},
-    {file = "CacheControl-0.12.14.tar.gz", hash = "sha256:d1087f45781c0e00616479bfd282c78504371ca71da017b49df9f5365a95feba"},
-]
-
-[package.dependencies]
-lockfile = {version = ">=0.9", optional = true, markers = "extra == \"filecache\""}
-msgpack = ">=0.5.2"
-requests = "*"
-
-[package.extras]
-filecache = ["lockfile (>=0.9)"]
-redis = ["redis (>=2.10.5)"]
-
 [[package]]
 name = "cachy"
-version = "0.3.0"
+version = "0.1.1"
 description = "Cachy provides a simple yet effective caching library."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = "*"
 files = [
-    {file = "cachy-0.3.0-py2.py3-none-any.whl", hash = "sha256:338ca09c8860e76b275aff52374330efedc4d5a5e45dc1c5b539c1ead0786fe7"},
-    {file = "cachy-0.3.0.tar.gz", hash = "sha256:186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1"},
+    {file = "cachy-0.1.1-py2.py3-none-any.whl", hash = "sha256:e52fade6799c16a7ebec481b83a857920c4d51dc1b40a63c82ce1af61766bc88"},
+    {file = "cachy-0.1.1.tar.gz", hash = "sha256:40b3ca1c57d0254c7d6d37920baadbb32a7e7cb7585e94f50764ad52ac016822"},
 ]
 
 [package.extras]
-memcached = ["python-memcached (>=1.59,<2.0)"]
-msgpack = ["msgpack-python (>=0.5,<0.6)"]
-redis = ["redis (>=3.3.6,<4.0.0)"]
+memcached = ["python-memcached"]
+memcachedc = ["pylibmc"]
+memcachedpy3 = ["python3-memcached"]
+redis = ["redis"]
 
 [[package]]
 name = "certifi"
@@ -163,70 +146,6 @@ files = [
     {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
 ]
 
-[[package]]
-name = "cffi"
-version = "1.16.0"
-description = "Foreign Function Interface for Python calling C code."
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "cffi-1.16.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:6b3d6606d369fc1da4fd8c357d026317fbb9c9b75d36dc16e90e84c26854b088"},
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-]
-
-[package.dependencies]
-pycparser = "*"
-
 [[package]]
 name = "charset-normalizer"
 version = "3.3.2"
@@ -328,23 +247,24 @@ files = [
 
 [[package]]
 name = "cleo"
-version = "0.7.6"
+version = "0.6.8"
 description = "Cleo allows you to create beautiful and testable command-line interfaces."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 files = [
-    {file = "cleo-0.7.6-py2.py3-none-any.whl", hash = "sha256:9443d67e5b2da79b32d820ae41758dd6a25618345cb10b9a022a695e26b291b9"},
-    {file = "cleo-0.7.6.tar.gz", hash = "sha256:99cf342406f3499cec43270fcfaf93c126c5164092eca201dfef0f623360b409"},
+    {file = "cleo-0.6.8-py2.py3-none-any.whl", hash = "sha256:9b7f79f1aa470a025c0d28c76aa225ee9e65028d32f80032e871aa3500df61b8"},
+    {file = "cleo-0.6.8.tar.gz", hash = "sha256:85a63076b72ca376fb06668be1fc7758dc16740b394783d5cc65200c4b32f71b"},
 ]
 
 [package.dependencies]
-clikit = ">=0.4.0,<0.5.0"
+pastel = ">=0.1.0,<0.2.0"
+pylev = ">=1.3,<2.0"
 
 [[package]]
 name = "click"
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 description = "Composable command line interface toolkit"
-optional = true
+optional = false
 python-versions = ">=3.7"
 files = [
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@@ -354,26 +274,11 @@ files = [
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
-[[package]]
-name = "clikit"
-version = "0.4.3"
-description = "CliKit is a group of utilities to build beautiful and testable command line interfaces."
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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-
-[package.dependencies]
-pastel = ">=0.2.0,<0.3.0"
-pylev = ">=1.3,<2.0"
-
 [[package]]
 name = "colorama"
 version = "0.4.6"
 description = "Cross-platform colored terminal text."
-optional = true
+optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
 files = [
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@@ -445,63 +350,61 @@ test-no-images = ["pytest", "pytest-cov", "pytest-xdist", "wurlitzer"]
 
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 name = "coverage"
-version = "7.3.3"
+version = "6.5.0"
 description = "Code coverage measurement for Python"
 optional = true
-python-versions = ">=3.8"
+python-versions = ">=3.7"
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 ]
 
 [package.dependencies]
@@ -512,68 +415,23 @@ toml = ["tomli"]
 
 [[package]]
 name = "coveralls"
-version = "1.8.0"
+version = "3.3.1"
 description = "Show coverage stats online via coveralls.io"
 optional = true
-python-versions = "*"
+python-versions = ">= 3.5"
 files = [
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+    {file = "coveralls-3.3.1.tar.gz", hash = "sha256:b32a8bb5d2df585207c119d6c01567b81fba690c9c10a753bfe27a335bfc43ea"},
 ]
 
 [package.dependencies]
-coverage = ">=3.6"
+coverage = ">=4.1,<6.0.dev0 || >6.1,<6.1.1 || >6.1.1,<7.0"
 docopt = ">=0.6.1"
 requests = ">=1.0.0"
 
 [package.extras]
 yaml = ["PyYAML (>=3.10)"]
 
-[[package]]
-name = "cryptography"
-version = "41.0.7"
-description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
-optional = false
-python-versions = ">=3.7"
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-
-[package.dependencies]
-cffi = ">=1.12"
-
-[package.extras]
-docs = ["sphinx (>=5.3.0)", "sphinx-rtd-theme (>=1.1.1)"]
-docstest = ["pyenchant (>=1.6.11)", "sphinxcontrib-spelling (>=4.0.1)", "twine (>=1.12.0)"]
-nox = ["nox"]
-pep8test = ["black", "check-sdist", "mypy", "ruff"]
-sdist = ["build"]
-ssh = ["bcrypt (>=3.1.5)"]
-test = ["pretend", "pytest (>=6.2.0)", "pytest-benchmark", "pytest-cov", "pytest-xdist"]
-test-randomorder = ["pytest-randomly"]
-
 [[package]]
 name = "cycler"
 version = "0.12.1"
@@ -658,6 +516,28 @@ files = [
     {file = "docutils-0.20.1.tar.gz", hash = "sha256:f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b"},
 ]
 
+[[package]]
+name = "elbow"
+version = "0.1.0"
+description = "Lift special-purpose data into common tabular formats for analytics 💪"
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "elbow-0.1.0-py3-none-any.whl", hash = "sha256:d060de2ae1ab1663d5d8b570351684d1050678fff31fcc2387f2d62a387e4f3a"},
+    {file = "elbow-0.1.0.tar.gz", hash = "sha256:4294086cc95925ed5ea0f61c9b0c52b0cb8496011a86002d48b6afd9d27ae92d"},
+]
+
+[package.dependencies]
+numpy = "*"
+pandas = "*"
+pyarrow = "*"
+tqdm = "*"
+typing-extensions = "*"
+
+[package.extras]
+dev = ["black (==23.3.0)", "flake8 (==5.0.4)", "isort (==5.11.5)", "mypy (==1.2.0)", "pre-commit", "pylint (>=2.5.0)", "setuptools-scm"]
+test = ["pytest", "pytest-benchmark", "pytest-cov"]
+
 [[package]]
 name = "exceptiongroup"
 version = "1.2.0"
@@ -672,6 +552,17 @@ files = [
 [package.extras]
 test = ["pytest (>=6)"]
 
+[[package]]
+name = "first"
+version = "2.0.2"
+description = "Return the first true value of an iterable."
+optional = false
+python-versions = "*"
+files = [
+    {file = "first-2.0.2-py2.py3-none-any.whl", hash = "sha256:8d8e46e115ea8ac652c76123c0865e3ff18372aef6f03c22809ceefcea9dec86"},
+    {file = "first-2.0.2.tar.gz", hash = "sha256:ff285b08c55f8c97ce4ea7012743af2495c9f1291785f163722bd36f6af6d3bf"},
+]
+
 [[package]]
 name = "fonttools"
 version = "4.47.0"
@@ -869,27 +760,6 @@ files = [
 [package.dependencies]
 numpy = ">=1.17.3"
 
-[[package]]
-name = "html5lib"
-version = "1.1"
-description = "HTML parser based on the WHATWG HTML specification"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-files = [
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-]
-
-[package.dependencies]
-six = ">=1.9"
-webencodings = "*"
-
-[package.extras]
-all = ["chardet (>=2.2)", "genshi", "lxml"]
-chardet = ["chardet (>=2.2)"]
-genshi = ["genshi"]
-lxml = ["lxml"]
-
 [[package]]
 name = "idna"
 version = "3.6"
@@ -953,21 +823,6 @@ files = [
     {file = "interface_meta-1.3.0.tar.gz", hash = "sha256:8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1"},
 ]
 
-[[package]]
-name = "jeepney"
-version = "0.8.0"
-description = "Low-level, pure Python DBus protocol wrapper."
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "jeepney-0.8.0-py3-none-any.whl", hash = "sha256:c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755"},
-    {file = "jeepney-0.8.0.tar.gz", hash = "sha256:5efe48d255973902f6badc3ce55e2aa6c5c3b3bc642059ef3a91247bcfcc5806"},
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-
-[package.extras]
-test = ["async-timeout", "pytest", "pytest-asyncio (>=0.17)", "pytest-trio", "testpath", "trio"]
-trio = ["async_generator", "trio"]
-
 [[package]]
 name = "jinja2"
 version = "3.1.2"
@@ -996,46 +851,6 @@ files = [
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 ]
 
-[[package]]
-name = "jsonschema"
-version = "3.2.0"
-description = "An implementation of JSON Schema validation for Python"
-optional = false
-python-versions = "*"
-files = [
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-]
-
-[package.dependencies]
-attrs = ">=17.4.0"
-pyrsistent = ">=0.14.0"
-setuptools = "*"
-six = ">=1.11.0"
-
-[package.extras]
-format = ["idna", "jsonpointer (>1.13)", "rfc3987", "strict-rfc3339", "webcolors"]
-format-nongpl = ["idna", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "webcolors"]
-
-[[package]]
-name = "keyring"
-version = "20.0.1"
-description = "Store and access your passwords safely."
-optional = false
-python-versions = ">=3.5"
-files = [
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-
-[package.dependencies]
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-secretstorage = {version = "*", markers = "sys_platform == \"linux\""}
-
-[package.extras]
-docs = ["jaraco.packaging (>=3.2)", "rst.linker (>=1.9)", "sphinx"]
-testing = ["pytest (>=3.5,!=3.7.3)", "pytest-black-multipy", "pytest-checkdocs (>=1.2.3)", "pytest-cov", "pytest-flake8"]
-
 [[package]]
 name = "kiwisolver"
 version = "1.4.5"
@@ -1149,17 +964,6 @@ files = [
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 ]
 
-[[package]]
-name = "lockfile"
-version = "0.12.2"
-description = "Platform-independent file locking module"
-optional = false
-python-versions = "*"
-files = [
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-]
-
 [[package]]
 name = "markdown-it-py"
 version = "3.0.0"
@@ -1312,71 +1116,6 @@ files = [
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 ]
 
-[[package]]
-name = "msgpack"
-version = "1.0.7"
-description = "MessagePack serializer"
-optional = false
-python-versions = ">=3.8"
-files = [
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@@ -1545,29 +1284,15 @@ xml = ["lxml (>=4.6.3)"]
 
 [[package]]
 name = "pastel"
-version = "0.2.1"
+version = "0.1.1"
 description = "Bring colors to your terminal."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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-[package.dependencies]
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@@ -1636,18 +1361,21 @@ docs = ["furo", "olefile", "sphinx (>=2.4)", "sphinx-copybutton", "sphinx-inline
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-description = "Query metadata from sdists / bdists / installed packages."
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-[package.extras]
-testing = ["pytest", "pytest-cov"]
+[package.dependencies]
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+first = "*"
+setuptools = "*"
+six = "*"
 
 [[package]]
 name = "pluggy"
@@ -1666,43 +1394,70 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
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+    {file = "pyarrow-14.0.2-cp312-cp312-win_amd64.whl", hash = "sha256:e4b123ad0f6add92de898214d404e488167b87b5dd86e9a434126bc2b7a5578d"},
+    {file = "pyarrow-14.0.2-cp38-cp38-macosx_10_14_x86_64.whl", hash = "sha256:e354fba8490de258be7687f341bc04aba181fc8aa1f71e4584f9890d9cb2dec2"},
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+    {file = "pyarrow-14.0.2-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:a51fee3a7db4d37f8cda3ea96f32530620d43b0489d169b285d774da48ca9785"},
+    {file = "pyarrow-14.0.2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:64df2bf1ef2ef14cee531e2dfe03dd924017650ffaa6f9513d7a1bb291e59c15"},
+    {file = "pyarrow-14.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3c0fa3bfdb0305ffe09810f9d3e2e50a2787e3a07063001dcd7adae0cee3601a"},
+    {file = "pyarrow-14.0.2-cp39-cp39-manylinux_2_28_aarch64.whl", hash = "sha256:c65bf4fd06584f058420238bc47a316e80dda01ec0dfb3044594128a6c2db794"},
+    {file = "pyarrow-14.0.2-cp39-cp39-manylinux_2_28_x86_64.whl", hash = "sha256:63ac901baec9369d6aae1cbe6cca11178fb018a8d45068aaf5bb54f94804a866"},
+    {file = "pyarrow-14.0.2-cp39-cp39-win_amd64.whl", hash = "sha256:75ee0efe7a87a687ae303d63037d08a48ef9ea0127064df18267252cfe2e9541"},
+    {file = "pyarrow-14.0.2.tar.gz", hash = "sha256:36cef6ba12b499d864d1def3e990f97949e0b79400d08b7cf74504ffbd3eb025"},
 ]
 
+[package.dependencies]
+numpy = ">=1.16.6"
+
 [[package]]
 name = "pybids"
 version = "0.16.4"
@@ -1736,17 +1491,6 @@ test = ["altair", "bsmschema", "coverage[toml]", "pytest (>=3.3)", "pytest-cov"]
 tests = ["pybids[test]"]
 tutorial = ["ipykernel", "jinja2", "jupyter-client", "markupsafe", "nbconvert"]
 
-[[package]]
-name = "pycparser"
-version = "2.21"
-description = "C parser in Python"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "pycparser-2.21-py2.py3-none-any.whl", hash = "sha256:8ee45429555515e1f6b185e78100aea234072576aa43ab53aefcae078162fca9"},
-    {file = "pycparser-2.21.tar.gz", hash = "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"},
-]
-
 [[package]]
 name = "pygments"
 version = "2.17.2"
@@ -1775,27 +1519,17 @@ files = [
 
 [[package]]
 name = "pyparsing"
-version = "2.4.7"
-description = "Python parsing module"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
-files = [
-    {file = "pyparsing-2.4.7-py2.py3-none-any.whl", hash = "sha256:ef9d7589ef3c200abe66653d3f1ab1033c3c419ae9b9bdb1240a85b024efc88b"},
-    {file = "pyparsing-2.4.7.tar.gz", hash = "sha256:c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1"},
-]
-
-[[package]]
-name = "pyrsistent"
-version = "0.14.11"
-description = "Persistent/Functional/Immutable data structures"
-optional = false
-python-versions = "*"
+version = "3.1.1"
+description = "pyparsing module - Classes and methods to define and execute parsing grammars"
+optional = true
+python-versions = ">=3.6.8"
 files = [
-    {file = "pyrsistent-0.14.11.tar.gz", hash = "sha256:3ca82748918eb65e2d89f222b702277099aca77e34843c5eb9d52451173970e2"},
+    {file = "pyparsing-3.1.1-py3-none-any.whl", hash = "sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb"},
+    {file = "pyparsing-3.1.1.tar.gz", hash = "sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db"},
 ]
 
-[package.dependencies]
-six = "*"
+[package.extras]
+diagrams = ["jinja2", "railroad-diagrams"]
 
 [[package]]
 name = "pytest"
@@ -1915,17 +1649,6 @@ files = [
     {file = "pywin32-306-cp39-cp39-win_amd64.whl", hash = "sha256:39b61c15272833b5c329a2989999dcae836b1eed650252ab1b7bfbe1d59f30f4"},
 ]
 
-[[package]]
-name = "pywin32-ctypes"
-version = "0.2.2"
-description = "A (partial) reimplementation of pywin32 using ctypes/cffi"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "pywin32-ctypes-0.2.2.tar.gz", hash = "sha256:3426e063bdd5fd4df74a14fa3cf80a0b42845a87e1d1e81f6549f9daec593a60"},
-    {file = "pywin32_ctypes-0.2.2-py3-none-any.whl", hash = "sha256:bf490a1a709baf35d688fe0ecf980ed4de11d2b3e37b51e5442587a75d9957e7"},
-]
-
 [[package]]
 name = "pyyaml"
 version = "6.0.1"
@@ -2006,20 +1729,6 @@ urllib3 = ">=1.21.1,<3"
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
-[[package]]
-name = "requests-toolbelt"
-version = "0.8.0"
-description = "A utility belt for advanced users of python-requests"
-optional = false
-python-versions = "*"
-files = [
-    {file = "requests-toolbelt-0.8.0.tar.gz", hash = "sha256:f6a531936c6fa4c6cfce1b9c10d5c4f498d16528d2a54a22ca00011205a187b5"},
-    {file = "requests_toolbelt-0.8.0-py2.py3-none-any.whl", hash = "sha256:42c9c170abc2cacb78b8ab23ac957945c7716249206f90874651971a4acff237"},
-]
-
-[package.dependencies]
-requests = ">=2.0.1,<3.0.0"
-
 [[package]]
 name = "rich"
 version = "13.7.0"
@@ -2128,21 +1837,6 @@ dev = ["click", "cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy", "pycodestyl
 doc = ["jupytext", "matplotlib (>2)", "myst-nb", "numpydoc", "pooch", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
 test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
-[[package]]
-name = "secretstorage"
-version = "3.3.3"
-description = "Python bindings to FreeDesktop.org Secret Service API"
-optional = false
-python-versions = ">=3.6"
-files = [
-    {file = "SecretStorage-3.3.3-py3-none-any.whl", hash = "sha256:f356e6628222568e3af06f2eba8df495efa13b3b63081dafd4f7d9a7b7bc9f99"},
-    {file = "SecretStorage-3.3.3.tar.gz", hash = "sha256:2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77"},
-]
-
-[package.dependencies]
-cryptography = ">=2.0"
-jeepney = ">=0.6"
-
 [[package]]
 name = "semver"
 version = "3.0.2"
@@ -2170,17 +1864,6 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments
 testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
-[[package]]
-name = "shellingham"
-version = "1.5.4"
-description = "Tool to Detect Surrounding Shell"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "shellingham-1.5.4-py2.py3-none-any.whl", hash = "sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686"},
-    {file = "shellingham-1.5.4.tar.gz", hash = "sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de"},
-]
-
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -2450,6 +2133,17 @@ files = [
     {file = "threadpoolctl-3.2.0.tar.gz", hash = "sha256:c96a0ba3bdddeaca37dc4cc7344aafad41cdb8c313f74fdfe387a867bba93355"},
 ]
 
+[[package]]
+name = "toml"
+version = "0.9.6"
+description = "Python Library for Tom's Obvious, Minimal Language"
+optional = false
+python-versions = "*"
+files = [
+    {file = "toml-0.9.6-py2.py3-none-any.whl", hash = "sha256:a7901919d3e4f92ffba7ff40a9d697e35bbbc8a8049fe8da742f34c83606d957"},
+    {file = "toml-0.9.6.tar.gz", hash = "sha256:380178cde50a6a79f9d2cf6f42a62a5174febe5eea4126fe4038785f1d888d42"},
+]
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
@@ -2461,17 +2155,6 @@ files = [
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
 
-[[package]]
-name = "tomlkit"
-version = "0.5.11"
-description = "Style preserving TOML library"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "tomlkit-0.5.11-py2.py3-none-any.whl", hash = "sha256:4e1bd6c9197d984528f9ff0cc9db667c317d8881288db50db20eeeb0f6b0380b"},
-    {file = "tomlkit-0.5.11.tar.gz", hash = "sha256:f044eda25647882e5ef22b43a1688fb6ab12af2fc50e8456cdfc751c873101cf"},
-]
-
 [[package]]
 name = "tornado"
 version = "6.4"
@@ -2492,6 +2175,51 @@ files = [
     {file = "tornado-6.4.tar.gz", hash = "sha256:72291fa6e6bc84e626589f1c29d90a5a6d593ef5ae68052ee2ef000dfd273dee"},
 ]
 
+[[package]]
+name = "tqdm"
+version = "4.66.1"
+description = "Fast, Extensible Progress Meter"
+optional = true
+python-versions = ">=3.7"
+files = [
+    {file = "tqdm-4.66.1-py3-none-any.whl", hash = "sha256:d302b3c5b53d47bce91fea46679d9c3c6508cf6332229aa1e7d8653723793386"},
+    {file = "tqdm-4.66.1.tar.gz", hash = "sha256:d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7"},
+]
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+
+[package.extras]
+dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+notebook = ["ipywidgets (>=6)"]
+slack = ["slack-sdk"]
+telegram = ["requests"]
+
+[[package]]
+name = "tsconcat"
+version = "0.1.0"
+description = "A beautiful description."
+optional = true
+python-versions = "^3.11"
+files = []
+develop = false
+
+[package.dependencies]
+bids2table = "^0.1.0a0"
+nibabel = "^5.2.0"
+numpy = "^1.25.1"
+pandas = "<2.2"
+rich = "^13.4.2"
+
+[package.extras]
+docs = ["pdoc (>=14.2.0,<15.0.0)"]
+
+[package.source]
+type = "git"
+url = "https://github.com/cmi-dair/tsconcat.git"
+reference = "HEAD"
+resolved_reference = "a7e31880431621fe47f48664df4736eb7a455859"
+
 [[package]]
 name = "typing-extensions"
 version = "4.9.0"
@@ -2571,17 +2299,6 @@ matplotlib = ">=2.0.0"
 numpy = ["numpy (>=1.9)"]
 web = ["wslink (>=1.0.4)"]
 
-[[package]]
-name = "webencodings"
-version = "0.5.1"
-description = "Character encoding aliases for legacy web content"
-optional = false
-python-versions = "*"
-files = [
-    {file = "webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78"},
-    {file = "webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923"},
-]
-
 [[package]]
 name = "websocket-client"
 version = "1.7.0"
@@ -2696,8 +2413,9 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
 dev = ["coveralls", "pytest", "pytest-remotedata", "pytest-runner", "sphinx"]
 gradients = ["ba_timeseries_gradients"]
 testing = ["alabaster", "imagesize", "pytest", "pytest-cov", "pytest-runner", "sphinx"]
+tsconcat = ["tsconcat"]
 
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8"
-content-hash = "16919655913a400e1161222084a751bf35cdc3dac7c6eed2e30db0dde28653ad"
+content-hash = "d047815286808ef52df4ab26f2a83cf1207a0c88f77c04a5dbfea997fc611ec6"
diff --git a/pyproject.toml b/pyproject.toml
index b07801b0..145f0c74 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -36,7 +36,10 @@ docker = ">=4.2.1"
 dockerpty = "*"
 docker-pycreds = "*"
 importlib_metadata = {version = "*", markers = "python_version < '3.8'"}
-pandas = ">=0.23.4"
+pandas = [
+  {version = ">=0.23.4"},
+  {version = "<2.1", markers = "extra == 'tsconcat'"}
+]
 poetry = "*"
 pyyaml = "*"
 rich = "*"
@@ -54,11 +57,13 @@ pytest-cov = {version = "*", optional = true}
 pytest-remotedata = {version = ">=0.3.2", optional = true}
 pytest-runner = {version = "*", optional = true}
 sphinx = {version = "*", optional = true}
+tsconcat = {git = "https://github.com/cmi-dair/tsconcat.git", optional = true, markers = "python_version >= '3.11' and python_version < '4.0'"}
 
 [tool.poetry.extras]
 dev = ["coveralls", "pytest", "pytest-remotedata", "pytest-runner", "sphinx"]
 gradients = ["ba_timeseries_gradients"]
 testing = ["alabaster", "imagesize", "pytest", "pytest-cov", "pytest-runner", "sphinx"]
+tsconcat = ["tsconcat"]
 
 [tool.poetry.scripts]
 cpac = "cpac.__main__:run"
diff --git a/src/cpac/__main__.py b/src/cpac/__main__.py
index af654920..f0a567cb 100644
--- a/src/cpac/__main__.py
+++ b/src/cpac/__main__.py
@@ -198,7 +198,7 @@ def _parser():
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
 
-    for bare_package in ["gradients"]:
+    for bare_package in ["gradients", "tsconcat"]:
         add_bare_wrapper(subparsers, bare_package)
 
     subparsers.add_parser(
diff --git a/src/cpac/utils/bare_wrap.py b/src/cpac/utils/bare_wrap.py
index 7d1504ba..77a97e4c 100644
--- a/src/cpac/utils/bare_wrap.py
+++ b/src/cpac/utils/bare_wrap.py
@@ -11,10 +11,11 @@ from sys import exit as sys_exit, version_info
 from typing import Optional, TypedDict
 
 if version_info.minor < 9:  # noqa: PLR2004
-    from typing import Dict, List
+    from typing import Dict, List, Tuple
 else:
     Dict = dict  # type: ignore
     List = list  # type: ignore
+    Tuple = tuple  # type: ignore
 
 from packaging.requirements import Requirement
 
@@ -23,8 +24,52 @@ try:
 except (ImportError, ModuleNotFoundError):
     gradients_parser = None
 
+try:
+    from tsconcat.utils import build_bidsapp_group_parser
+except (ImportError, ModuleNotFoundError):
+    tsconcat_parser = build_bidsapp_group_parser = None
+
 from cpac.utils import INTERVAL_CHECKS, version_tuple
 
+if build_bidsapp_group_parser is not None:
+    """
+    This parser is built in the main function of the wrapped package https://github.com/cmi-dair/tsconcat/blob/a7e31880431621fe47f48664df4736eb7a455859/src/tsconcat/cli.py#L78C14-L104 , so we recreate it here to generate the usage string for the wrapper."""
+    from tsconcat.cli import REDUCE_COLUMNS
+
+    tsconcat_parser = build_bidsapp_group_parser(
+        prog="ba-tsconcat", description="Concatenate MRI timeseries."
+    )
+    tsconcat_parser.add_argument(
+        "-c",
+        "--concat",
+        type=str,
+        help=f"Concat across. Can be any combination of {', '.join(REDUCE_COLUMNS)} separated by spaces. "
+        f"Output data will be grouped by the set difference.",
+        default="ses",
+    )
+    tsconcat_parser.add_argument(
+        "-d",
+        "--dry_run",
+        action="store_true",
+        help="Dry run. Print output directory structure instead of actually doing something. "
+        "If this is enabled 'bids_dir' may be a path to a bids2table parquet directory.",
+        default=False,
+    )
+    tsconcat_parser.add_argument(
+        "-f",
+        "--fake",
+        action="store_true",
+        help="Fake output. Output a bids2table parquet directory instead of actually doing something.",
+        default=False,
+    )
+
+_PARSERS = {
+    "gradients": gradients_parser()
+    if gradients_parser is not None
+    else gradients_parser,
+    "tsconcat": tsconcat_parser,
+}
+"""CLI parsers for wrapped packages"""
 WRAPPED = {}
 """memoization of wrapped packages"""
 
@@ -36,6 +81,8 @@ class ScriptInfo(TypedDict):
     """The command to run."""
     helpstring: Optional[str]
     """The original usage string."""
+    package: str
+    """The canonical name of the wrapped package."""
     positional_arguments: bool
     """Whether the original command takes positional arguments."""
     supported_python: str
@@ -48,10 +95,19 @@ _SCRIPTS: Dict[str, ScriptInfo] = {
     "gradients": {
         "command": "ba_timeseries_gradients",
         "helpstring": None,
+        "package": "ba_timeseries_gradients",
         "positional_arguments": True,
         "supported_python": "[3.11, 3.12)",
         "url": "https://cmi-dair.github.io/ba-timeseries-gradients/ba_timeseries_gradients.html",
-    }
+    },
+    "tsconcat": {
+        "command": "ba-tsconcat",
+        "helpstring": None,
+        "package": "tsconcat",
+        "positional_arguments": True,
+        "supported_python": "[3.11, 4.0)",
+        "url": "https://cmi-dair.github.io/tsconcat/tsconcat.html",
+    },
 }
 """Info needed for bare package wrapping."""
 
@@ -66,6 +122,8 @@ class WrappedBare:
     """The wrapped command."""
     _helpstring: Optional[str]
     """The original usage string."""
+    package: str
+    """The canonical name of the wrapped package."""
     positional_arguments: bool
     """Whether the original command takes positional arguments."""
     supported_python_range: str
@@ -80,13 +138,23 @@ class WrappedBare:
             if not self.supported_python:
                 self._helpstring = f"Extra command '{self.name}' not supported on Python {f'{version_info.major}.{version_info.minor}.{ version_info.micro}'}; supported Python versions range is {self.supported_python_range}.\n\nSee {self.url} for more information and system requirements."
             else:
-                self._helpstring = f"Extra script {self.command} not found. See {self.url} for more information and system requirements, or run `pip install cpac[{self.name}]` to try to install it."
+                self._helpstring = f"Extra package {self.package} not found. See {self.url} for more information and system requirements, or run `pip install cpac[{self.name}]` to try to install it."
         return self._helpstring.replace(f"usage: {self.command}", f"cpac {self.name}")
 
     @property
-    def supported_python(self):
+    def split_range(self) -> Tuple[str, str]:
+        """Split the supported Python range into min and max."""
+        if not hasattr(self, "_split_range"):
+            py_min, py_max = (
+                _.strip() for _ in self.supported_python_range.split(",", 1)
+            )
+            self._split_range = (py_min, py_max)
+        return self._split_range
+
+    @property
+    def supported_python(self) -> bool:
         """Whether the wrapped package supports the current Python version."""
-        py_min, py_max = [_.strip() for _ in self.supported_python_range.split(",")]
+        py_min, py_max = self.split_range
         return getattr(version_info, INTERVAL_CHECKS[py_min[0]])(
             version_tuple(py_min[1:])
         ) and getattr(version_info, INTERVAL_CHECKS[py_max[-1]])(
@@ -142,7 +210,7 @@ def call(name: str, command: list) -> None:
     requirements: Dict[str, Requirement] = {req.name: req for req in _requirements}
     del _requirements
     try:
-        package_info = requirements[script.command]
+        package_info = requirements[script.package]
     except KeyError as ke:
         raise KeyError(f"Package {name} not defined in dependencies") from ke
     marker = getattr(package_info, "marker", None)
@@ -163,6 +231,15 @@ def check_for_package(package_name: str) -> bool:
     return which(package_name) is not None
 
 
+def _collect_usage_string(name: str) -> None:
+    """Collect a usage string from a wrapped package to use in the helpstring."""
+    if _PARSERS[name] is not None:
+        try:
+            _SCRIPTS[name]["helpstring"] = _PARSERS[name].format_help()
+        except AttributeError:
+            print(name)
+
+
 def get_wrapped(name: str) -> WrappedBare:
     """Get the name of the script to run.
 
@@ -177,13 +254,13 @@ def get_wrapped(name: str) -> WrappedBare:
         The name of the script to run
     """
     if name not in WRAPPED:
-        if gradients_parser is not None:
-            _SCRIPTS["gradients"]["helpstring"] = gradients_parser().format_help()
+        _collect_usage_string(name)
         if name in _SCRIPTS:
             WRAPPED[name] = WrappedBare(
                 name,
                 _SCRIPTS[name]["command"],
                 _SCRIPTS[name]["helpstring"],
+                _SCRIPTS[name]["package"],
                 _SCRIPTS[name]["positional_arguments"],
                 _SCRIPTS[name]["supported_python"],
                 _SCRIPTS[name]["url"],


Test patch:
diff --git a/.github/workflows/test_cpac.yml b/.github/workflows/test_cpac.yml
index 30223c62..8231f5a5 100644
--- a/.github/workflows/test_cpac.yml
+++ b/.github/workflows/test_cpac.yml
@@ -46,7 +46,7 @@ jobs:
       if: ${{ matrix.platform == 'singularity' }}
       run: mkdir -p ${SINGULARITY_CACHEDIR} && mkdir -p ${SINGULARITY_TMPDIR}
     - name: Install cpac
-      run: cd $GITHUB_WORKSPACE && pip install -e ".[dev,gradients,testing]"
+      run: cd $GITHUB_WORKSPACE && pip install -e ".[dev,gradients,testing,tsconcat]"
     - name: Test cpac, platform and tag specified
       run: |
         coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --platform ${{ matrix.platform }} --tag ${{ matrix.tag }} .