From af4fa95340aa7196cd3e202a4bc45fd0bdde01af Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 16:14:01 +0100
Subject: [PATCH 01/37] Adds _version.py

---
 nii2dcm/_version.py | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 nii2dcm/_version.py

diff --git a/nii2dcm/_version.py b/nii2dcm/_version.py
new file mode 100644
index 0000000..1f5b08c
--- /dev/null
+++ b/nii2dcm/_version.py
@@ -0,0 +1 @@
+__version__ = '0.1.2dev1'

From d86e897fa560c99b4afa84a605cdec2dd9b9a564 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 16:14:26 +0100
Subject: [PATCH 02/37] Correctly name pyproject.toml

---
 pyprojects.toml => pyproject.toml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename pyprojects.toml => pyproject.toml (100%)

diff --git a/pyprojects.toml b/pyproject.toml
similarity index 100%
rename from pyprojects.toml
rename to pyproject.toml

From c76f1bf1de27430d6b1036e3f72b2d5cff39eac3 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 16:47:42 +0100
Subject: [PATCH 03/37] Replaces setup.py with setup.cfg

---
 setup.cfg | 23 +++++++++++++++++++++++
 setup.py  | 30 ------------------------------
 2 files changed, 23 insertions(+), 30 deletions(-)
 create mode 100644 setup.cfg
 delete mode 100644 setup.py

diff --git a/setup.cfg b/setup.cfg
new file mode 100644
index 0000000..7f217d6
--- /dev/null
+++ b/setup.cfg
@@ -0,0 +1,23 @@
+[metadata]
+name = nii2dcm
+version = attr: nii2dcm._version.__version__
+description= nii2dcm: NIfTI to DICOM creation with Python
+url = https://github.com/tomaroberts/nii2dcm
+author = Tom Roberts
+author_email = t.roberts@kcl.ac.uk
+long_description = file:README.md
+long_description_content_type = text/markdown
+
+[options]
+packages = find:
+python_requires = <3.11
+install_requires =
+    numpy
+    matplotlib
+    nibabel
+    pydicom
+include_package_data=True
+
+[options.entry_points]
+console_scripts =
+    nii2dcm = nii2dcm.__main__:cli
\ No newline at end of file
diff --git a/setup.py b/setup.py
deleted file mode 100644
index cada10e..0000000
--- a/setup.py
+++ /dev/null
@@ -1,30 +0,0 @@
-from setuptools import setup, find_packages
-from pathlib import Path
-
-
-# import README.md for long_description
-this_directory = Path(__file__).parent
-long_description = (this_directory / "README.md").read_text()
-
-setup(
-    name="nii2dcm",
-    version="0.1.1",
-    description='nii2dcm: NIfTI to DICOM creation with Python',
-    author='Tom Roberts',
-    url='https://github.com/tomaroberts/nii2dcm',
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    packages=find_packages(include=['nii2dcm', 'nii2dcm.*']),
-    install_requires=[
-        'numpy',
-        'matplotlib',
-        'nibabel',
-        'pydicom'
-    ],
-    setup_requires=['flake8'],
-    entry_points={
-        "console_scripts": [
-            "nii2dcm = nii2dcm.__main__:cli"
-        ]
-    },
-)
\ No newline at end of file

From 11c72e02026a1cc83180075d434b680f04c9a023 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 16:48:09 +0100
Subject: [PATCH 04/37] Strips back pyproject.toml so package contents in
 setup.cfg

---
 pyproject.toml | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9446c82..1d284e0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,13 +1,3 @@
 [build-system]
 requires = ["setuptools>=64.0.0", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "nii2dcm"
-version = "0.1.0"
-description = "NIfTI file to DICOM conversion"
-readme = "README.md"
-authors = [{ name = "Tom Roberts", email = "t.roberts@kcl.ac.uk" }]
-
-[project.scripts]
-nii2dcm = "nii2dcm.__main__:cli"
\ No newline at end of file
+build-backend = "setuptools.build_meta"
\ No newline at end of file

From 57fa9d383f2b6bcfb528c1f662760bb12c063738 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 16:48:24 +0100
Subject: [PATCH 05/37] Updates main to use _version.py

---
 nii2dcm/__main__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nii2dcm/__main__.py b/nii2dcm/__main__.py
index 994afe2..de57792 100644
--- a/nii2dcm/__main__.py
+++ b/nii2dcm/__main__.py
@@ -6,6 +6,7 @@
 import argparse
 from pathlib import Path
 from nii2dcm.run import run_nii2dcm
+from nii2dcm._version import __version__
 
 
 def cli(args=None):
@@ -24,7 +25,7 @@ def cli(args=None):
     parser.add_argument("output_dir", type=str, help="[directory] output DICOM path")
     parser.add_argument("-d", "--dicom_type", type=str, help="[string] type of DICOM. e.g. MR, CT, US, XR, etc.")
     parser.add_argument("-r", "--ref_dicom", type=str, help="[.dcm] Reference DICOM file for Attribute transfer")
-    parser.add_argument("-v", "--version", action="version", version="0.1.0")
+    parser.add_argument("-v", "--version", action="version", version=__version__)
 
     args = parser.parse_args()
 

From 8959253500c62e8bf997f7ed529e5cee1887e770 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 16:57:51 +0100
Subject: [PATCH 06/37] Update .gitignore

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index d7c3b9c..1a1bd68 100644
--- a/.gitignore
+++ b/.gitignore
@@ -88,5 +88,8 @@ _im*
 *.nii
 *.nii.gz
 
+# Omit _version.py as required by setuptools_scm
+!nii2dcm/_version.py
+
 # Permit Test Data
 !tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz
\ No newline at end of file

From bf1e37126df66c377982a70fe67f67a881d0e5d1 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 16:59:45 +0100
Subject: [PATCH 07/37] Delete _version.py as setuptools_scm generates
 dynamically

---
 nii2dcm/_version.py | 1 -
 1 file changed, 1 deletion(-)
 delete mode 100644 nii2dcm/_version.py

diff --git a/nii2dcm/_version.py b/nii2dcm/_version.py
deleted file mode 100644
index 1f5b08c..0000000
--- a/nii2dcm/_version.py
+++ /dev/null
@@ -1 +0,0 @@
-__version__ = '0.1.2dev1'

From 8738bc844c1b2b2c3fda82ea35766a42dcd9a38a Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 17:00:40 +0100
Subject: [PATCH 08/37] Bugfix: updates .gitignore

---
 .gitignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 1a1bd68..b0f0c11 100644
--- a/.gitignore
+++ b/.gitignore
@@ -89,7 +89,7 @@ _im*
 *.nii.gz
 
 # Omit _version.py as required by setuptools_scm
-!nii2dcm/_version.py
+nii2dcm/_version.py
 
 # Permit Test Data
 !tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz
\ No newline at end of file

From 28c17576a13c4c9b5bf228cddc898afce318669b Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 17:01:25 +0100
Subject: [PATCH 09/37] Updates pyproject.toml to use setuptools_scm dynamic
 versioning

---
 pyproject.toml | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1d284e0..f885137 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,10 @@
 [build-system]
-requires = ["setuptools>=64.0.0", "wheel"]
-build-backend = "setuptools.build_meta"
\ No newline at end of file
+requires = ["setuptools>=64.0.0", "wheel", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nii2dcm"
+dynamic = ["version"]
+
+[tool.setuptools_scm]
+write_to = "nii2dcm/_version.py"
\ No newline at end of file

From 451dd1873cc0346153a08026c44cf22c1e33c7f6 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 17:34:54 +0100
Subject: [PATCH 10/37] Use setuptools_scm "no-local-version" local_scheme for
 PyPI compatibility

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index f885137..e06e019 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,4 +7,5 @@ name = "nii2dcm"
 dynamic = ["version"]
 
 [tool.setuptools_scm]
+local_scheme = "no-local-version"  # required for PyPI and TestPyPI
 write_to = "nii2dcm/_version.py"
\ No newline at end of file

From ff83508b66c6de76830ab7aa2142d416c29cfdfc Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 17:35:21 +0100
Subject: [PATCH 11/37] Creates TestPyPI GitHub Action

---
 .github/workflows/publish_testpypi.yml | 54 ++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 .github/workflows/publish_testpypi.yml

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
new file mode 100644
index 0000000..697427d
--- /dev/null
+++ b/.github/workflows/publish_testpypi.yml
@@ -0,0 +1,54 @@
+# Publish to TestPyPI
+#
+# This workflow publishes nii2dcm on TestPyPI prior to production release onto PyPI. The workflow is intended to catch
+# any issues arising during the release procedure to prevent unnecessary versioning issues on PyPI
+#
+# This workflow will upload a Python Package using Twine when a release is created. For more information see:
+# https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+#
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Publish package to TestPyPI
+
+on:
+  pull_request
+
+permissions:
+  contents: read
+
+jobs:
+  testpypi-publish:
+
+    name: Publish release to TestPyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/nii2dcm
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for PyPI trusted publishing
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+
+    - name: Build package
+      run: python -m build
+
+    - name: Publish package to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.TESTPYPI_API_TOKEN }}
+        verbose: true
\ No newline at end of file

From 945409af3eb63163db1eac6ef80ef8d39ffd85bf Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 18:10:06 +0100
Subject: [PATCH 12/37] Bugfix: adds TestPyPI repository-url to GHA

---
 .github/workflows/publish_testpypi.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 697427d..0a687f8 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -51,4 +51,5 @@ jobs:
       with:
         user: __token__
         password: ${{ secrets.TESTPYPI_API_TOKEN }}
+        repository-url: https://test.pypi.org/legacy/
         verbose: true
\ No newline at end of file

From af4242f110c57158e85e29efdda3b8f7d67e52b7 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 18:12:33 +0100
Subject: [PATCH 13/37] Trivial change to test GHA version incrementing

---
 .github/workflows/publish_testpypi.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 0a687f8..3ba8ad5 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -52,4 +52,4 @@ jobs:
         user: __token__
         password: ${{ secrets.TESTPYPI_API_TOKEN }}
         repository-url: https://test.pypi.org/legacy/
-        verbose: true
\ No newline at end of file
+        verbose: true

From f7b21a44f2db645f0b139bceb6f94c706f0c3377 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Tue, 22 Aug 2023 18:17:44 +0100
Subject: [PATCH 14/37] GHA Test: enable _version.py to be committed to see
 versioning on TestPyPI

---
 .gitignore          | 3 ---
 nii2dcm/_version.py | 4 ++++
 2 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 nii2dcm/_version.py

diff --git a/.gitignore b/.gitignore
index b0f0c11..d7c3b9c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -88,8 +88,5 @@ _im*
 *.nii
 *.nii.gz
 
-# Omit _version.py as required by setuptools_scm
-nii2dcm/_version.py
-
 # Permit Test Data
 !tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz
\ No newline at end of file
diff --git a/nii2dcm/_version.py b/nii2dcm/_version.py
new file mode 100644
index 0000000..91d9133
--- /dev/null
+++ b/nii2dcm/_version.py
@@ -0,0 +1,4 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+__version__ = version = '0.1.2.dev22'
+__version_tuple__ = version_tuple = (0, 1, 2, 'dev22')

From 503f3f1ee1c52882906df2f22a2a34c49e0cad82 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Wed, 23 Aug 2023 08:44:26 +0100
Subject: [PATCH 15/37] Add CLI version command test to GHA

---
 .github/workflows/build_and_test_cli.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/build_and_test_cli.yml b/.github/workflows/build_and_test_cli.yml
index 7a9a5f9..d707658 100644
--- a/.github/workflows/build_and_test_cli.yml
+++ b/.github/workflows/build_and_test_cli.yml
@@ -56,6 +56,7 @@ jobs:
     - name: Test nii2dcm install
       run: |
         nii2dcm -h
+        nii2dcm -v
 
     - name: Test DicomMRISVR creation
       run: |

From 3915849d203e84a364916b94d1635131a9172f92 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 13:03:23 +0100
Subject: [PATCH 16/37] GHA test: python build --sdist --wheel

---
 .github/workflows/publish_testpypi.yml | 2 +-
 nii2dcm/_version.py                    | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 3ba8ad5..f6e5813 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -41,7 +41,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install build
+        pip install build --sdist --wheel --outdir dist/
 
     - name: Build package
       run: python -m build
diff --git a/nii2dcm/_version.py b/nii2dcm/_version.py
index 91d9133..7419e0a 100644
--- a/nii2dcm/_version.py
+++ b/nii2dcm/_version.py
@@ -1,4 +1,4 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '0.1.2.dev22'
-__version_tuple__ = version_tuple = (0, 1, 2, 'dev22')
+__version__ = version = '0.1.2.dev27'
+__version_tuple__ = version_tuple = (0, 1, 2, 'dev27')

From 9ba81a288af9b4151def0f09a1b0719252e488e1 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 13:06:54 +0100
Subject: [PATCH 17/37] =?UTF-8?q?Fix=20error=20=E2=80=93=20re-run=20previo?=
 =?UTF-8?q?us=20GHA?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .github/workflows/publish_testpypi.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index f6e5813..67b2304 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -41,10 +41,10 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install build --sdist --wheel --outdir dist/
+        pip install build
 
     - name: Build package
-      run: python -m build
+      run: python -m build --sdist --wheel --outdir dist/
 
     - name: Publish package to TestPyPI
       uses: pypa/gh-action-pypi-publish@release/v1

From 5b3ee760c4fb99f9e8dfc17d7b1eba0703aa9eae Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 13:11:01 +0100
Subject: [PATCH 18/37] GHA test: adds skip-existing option when publishing on
 TestPyPI

---
 .github/workflows/publish_testpypi.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 67b2304..bb9d7d6 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -53,3 +53,4 @@ jobs:
         password: ${{ secrets.TESTPYPI_API_TOKEN }}
         repository-url: https://test.pypi.org/legacy/
         verbose: true
+        skip-existing: true

From 79493b46210f2dbd0b74a0c0d61eccffe261fc63 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 13:25:14 +0100
Subject: [PATCH 19/37] GHA test: manual update of __version__

---
 nii2dcm/_version.py |  3 +--
 pyproject.toml      | 14 +++++++-------
 2 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/nii2dcm/_version.py b/nii2dcm/_version.py
index 7419e0a..dd19a1b 100644
--- a/nii2dcm/_version.py
+++ b/nii2dcm/_version.py
@@ -1,4 +1,3 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '0.1.2.dev27'
-__version_tuple__ = version_tuple = (0, 1, 2, 'dev27')
+__version__ = version = '0.1.dev2'
diff --git a/pyproject.toml b/pyproject.toml
index e06e019..e7cf0a3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,10 +2,10 @@
 requires = ["setuptools>=64.0.0", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
-[project]
-name = "nii2dcm"
-dynamic = ["version"]
-
-[tool.setuptools_scm]
-local_scheme = "no-local-version"  # required for PyPI and TestPyPI
-write_to = "nii2dcm/_version.py"
\ No newline at end of file
+# [project]
+# name = "nii2dcm"
+# dynamic = ["version"]
+#
+# [tool.setuptools_scm]
+# local_scheme = "no-local-version"  # required for PyPI and TestPyPI
+# write_to = "nii2dcm/_version.py"
\ No newline at end of file

From 2b37c36e75f59e1dce8514e1eb3e5759ab81ceec Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 13:44:20 +0100
Subject: [PATCH 20/37] Revert "GHA test: adds skip-existing option when
 publishing on TestPyPI"

This reverts commit 5b3ee760c4fb99f9e8dfc17d7b1eba0703aa9eae.
---
 .github/workflows/publish_testpypi.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index bb9d7d6..67b2304 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -53,4 +53,3 @@ jobs:
         password: ${{ secrets.TESTPYPI_API_TOKEN }}
         repository-url: https://test.pypi.org/legacy/
         verbose: true
-        skip-existing: true

From 8269cae47c522bc48b63aced78de61868318a216 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 13:44:54 +0100
Subject: [PATCH 21/37] Test GHA: reinstate setuptools-scm

---
 pyproject.toml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e7cf0a3..e06e019 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -2,10 +2,10 @@
 requires = ["setuptools>=64.0.0", "wheel", "setuptools_scm[toml]>=6.2"]
 build-backend = "setuptools.build_meta"
 
-# [project]
-# name = "nii2dcm"
-# dynamic = ["version"]
-#
-# [tool.setuptools_scm]
-# local_scheme = "no-local-version"  # required for PyPI and TestPyPI
-# write_to = "nii2dcm/_version.py"
\ No newline at end of file
+[project]
+name = "nii2dcm"
+dynamic = ["version"]
+
+[tool.setuptools_scm]
+local_scheme = "no-local-version"  # required for PyPI and TestPyPI
+write_to = "nii2dcm/_version.py"
\ No newline at end of file

From 029d4be7a688609bf53473702f35d5dfaea51489 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 13:45:37 +0100
Subject: [PATCH 22/37] Update .gitignore

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index d7c3b9c..b0f0c11 100644
--- a/.gitignore
+++ b/.gitignore
@@ -88,5 +88,8 @@ _im*
 *.nii
 *.nii.gz
 
+# Omit _version.py as required by setuptools_scm
+nii2dcm/_version.py
+
 # Permit Test Data
 !tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz
\ No newline at end of file

From 7bf1977ec2bcc240249f79f5f1f81026ddcd6a53 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 13:58:22 +0100
Subject: [PATCH 23/37] Test GHA: use fetch-depth 0

---
 .github/workflows/publish_testpypi.yml | 2 ++
 nii2dcm/_version.py                    | 3 ---
 2 files changed, 2 insertions(+), 3 deletions(-)
 delete mode 100644 nii2dcm/_version.py

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 67b2304..380bf59 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -32,6 +32,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
 
     - name: Set up Python
       uses: actions/setup-python@v4
diff --git a/nii2dcm/_version.py b/nii2dcm/_version.py
deleted file mode 100644
index dd19a1b..0000000
--- a/nii2dcm/_version.py
+++ /dev/null
@@ -1,3 +0,0 @@
-# file generated by setuptools_scm
-# don't change, don't track in version control
-__version__ = version = '0.1.dev2'

From aa7072bbb72c314cb032c85cc2fd5e275721ba17 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 14:13:34 +0100
Subject: [PATCH 24/37] GHA Test: display version in GHA for debugging

---
 .github/workflows/publish_testpypi.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 380bf59..eb67bb6 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -48,6 +48,11 @@ jobs:
     - name: Build package
       run: python -m build --sdist --wheel --outdir dist/
 
+    - name: Display nii2dcm version
+      run: |
+        echo "nii2dcm version:"
+        nii2dcm -v
+
     - name: Publish package to TestPyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

From e4222b1f202e8c9c63cd8f3ac7b4a8a6cff6a996 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 14:16:49 +0100
Subject: [PATCH 25/37] Update publish_testpypi.yml

---
 .github/workflows/publish_testpypi.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index eb67bb6..be6e3ed 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -50,6 +50,7 @@ jobs:
 
     - name: Display nii2dcm version
       run: |
+        pip install -e .
         echo "nii2dcm version:"
         nii2dcm -v
 

From 3c87e59e01ceda75ba4f8fdfa779f46ba8bf96ad Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 14:26:08 +0100
Subject: [PATCH 26/37] Update setup.cfg install_requires

pip install breaking otherwise - can't find matplotlib version
---
 setup.cfg | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 7f217d6..ecb4ce5 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -12,10 +12,10 @@ long_description_content_type = text/markdown
 packages = find:
 python_requires = <3.11
 install_requires =
-    numpy
-    matplotlib
-    nibabel
-    pydicom
+    numpy ~= 1.23.2
+    matplotlib ~= 3.6.2
+    nibabel ~= 5.0.0
+    pydicom ~= 2.3.0
 include_package_data=True
 
 [options.entry_points]

From caf5051849d8c10a1de3dd76d0ba04462cc5466b Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 14:34:38 +0100
Subject: [PATCH 27/37] Fix dependency versions in setup.cfg

---
 setup.cfg | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index ecb4ce5..1a38b92 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -12,10 +12,11 @@ long_description_content_type = text/markdown
 packages = find:
 python_requires = <3.11
 install_requires =
-    numpy ~= 1.23.2
-    matplotlib ~= 3.6.2
-    nibabel ~= 5.0.0
-    pydicom ~= 2.3.0
+    numpy==1.23.2
+    matplotlib==3.6.2
+    nibabel==5.0.0
+    pydicom==2.3.0
+    twine==4.0.2
 include_package_data=True
 
 [options.entry_points]

From 51e3cf4ce3b667afa91130140281a5f6dce562c6 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 15:02:26 +0100
Subject: [PATCH 28/37] GHA Test: verify TestPyPI build in fresh venv

---
 .github/workflows/publish_testpypi.yml | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index be6e3ed..20ae570 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -49,10 +49,12 @@ jobs:
       run: python -m build --sdist --wheel --outdir dist/
 
     - name: Display nii2dcm version
+      id: nii2dcm-version
       run: |
         pip install -e .
         echo "nii2dcm version:"
         nii2dcm -v
+        echo "{NII2DCM_VERSION}={nii2dcm -v}" >> "$GITHUB_OUTPUT"
 
     - name: Publish package to TestPyPI
       uses: pypa/gh-action-pypi-publish@release/v1
@@ -61,3 +63,19 @@ jobs:
         password: ${{ secrets.TESTPYPI_API_TOKEN }}
         repository-url: https://test.pypi.org/legacy/
         verbose: true
+
+    - name: Wait to allow TestPyPI to update
+      uses: GuillaumeFalourd/wait-sleep-action@v1
+        with:
+          time: '1m'
+
+    - name: Install latest TestPyPI version in fresh venv
+      env:
+        NII2DCM_VERSION: ${{ steps.nii2dcm-version.outputs.NII2DCM_VERSION }}
+      run: |
+        deactivate
+        python -m venv n2d
+        source n2d/bin/activate
+        pip install --upgrade pip
+        pip install setuptools wheel
+        pip install --extra-url-index https://test.pypi.org/simple/ nii2dcm==$NII2DCM_VERSION

From 1a411cd7204dfcdfd0f36c0c10d69226d4e32c77 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:08:01 +0100
Subject: [PATCH 29/37] Get and pass version nii2dcm version with bash echo

---
 .github/workflows/publish_testpypi.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 20ae570..25534a9 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -54,7 +54,6 @@ jobs:
         pip install -e .
         echo "nii2dcm version:"
         nii2dcm -v
-        echo "{NII2DCM_VERSION}={nii2dcm -v}" >> "$GITHUB_OUTPUT"
 
     - name: Publish package to TestPyPI
       uses: pypa/gh-action-pypi-publish@release/v1
@@ -70,9 +69,8 @@ jobs:
           time: '1m'
 
     - name: Install latest TestPyPI version in fresh venv
-      env:
-        NII2DCM_VERSION: ${{ steps.nii2dcm-version.outputs.NII2DCM_VERSION }}
       run: |
+        NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
         deactivate
         python -m venv n2d
         source n2d/bin/activate

From 480dc4960fbd617da431bb85eb569aa0d67c6a19 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:10:17 +0100
Subject: [PATCH 30/37] Fixes yaml syntax error

---
 .github/workflows/publish_testpypi.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 25534a9..cb1531a 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -65,8 +65,8 @@ jobs:
 
     - name: Wait to allow TestPyPI to update
       uses: GuillaumeFalourd/wait-sleep-action@v1
-        with:
-          time: '1m'
+      with:
+        time: '1m'
 
     - name: Install latest TestPyPI version in fresh venv
       run: |

From 668f0f42a4d140a107fd217347ccef577642f21b Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:15:25 +0100
Subject: [PATCH 31/37] Test GHA: remove erroneous deactivate line

---
 .github/workflows/publish_testpypi.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index cb1531a..caa2aae 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -71,9 +71,8 @@ jobs:
     - name: Install latest TestPyPI version in fresh venv
       run: |
         NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
-        deactivate
-        python -m venv n2d
-        source n2d/bin/activate
+        python -m venv nii2dcm-temp
+        source nii2dcm-temp/bin/activate
         pip install --upgrade pip
         pip install setuptools wheel
         pip install --extra-url-index https://test.pypi.org/simple/ nii2dcm==$NII2DCM_VERSION

From e39ef9029c9375e4079edbe56ec7baa9d351c8d7 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:21:21 +0100
Subject: [PATCH 32/37] Update publish_testpypi.yml

---
 .github/workflows/publish_testpypi.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index caa2aae..5d0c398 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -71,8 +71,9 @@ jobs:
     - name: Install latest TestPyPI version in fresh venv
       run: |
         NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
+        echo $NII2DCM_VERSION
         python -m venv nii2dcm-temp
         source nii2dcm-temp/bin/activate
         pip install --upgrade pip
         pip install setuptools wheel
-        pip install --extra-url-index https://test.pypi.org/simple/ nii2dcm==$NII2DCM_VERSION
+        pip install --index-url https://test.pypi.org/simple/ nii2dcm==$NII2DCM_VERSION

From 03371218877a64c692878e0e115bbdc3489800ed Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:25:22 +0100
Subject: [PATCH 33/37] Pull nii2dcm from TestPyPI / allow dependencies from
 PyPI

---
 .github/workflows/publish_testpypi.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 5d0c398..75c0496 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -76,4 +76,4 @@ jobs:
         source nii2dcm-temp/bin/activate
         pip install --upgrade pip
         pip install setuptools wheel
-        pip install --index-url https://test.pypi.org/simple/ nii2dcm==$NII2DCM_VERSION
+        pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ nii2dcm==$NII2DCM_VERSION

From d0ab098f23f33776fe6674a7ec028788eae2c9e2 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:29:05 +0100
Subject: [PATCH 34/37] Add nii2dcm -h test to verify working

---
 .github/workflows/publish_testpypi.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 75c0496..f59f938 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -77,3 +77,4 @@ jobs:
         pip install --upgrade pip
         pip install setuptools wheel
         pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ nii2dcm==$NII2DCM_VERSION
+        nii2dcm -h

From 95b8f1551f83c38c1b72adcaa5d9b8a213775b45 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:36:50 +0100
Subject: [PATCH 35/37] Fixes some linting warnings

---
 .github/workflows/publish_testpypi.yml | 2 ++
 nii2dcm/modules/image_pixel.py         | 6 +++---
 nii2dcm/nii.py                         | 2 +-
 scripts/create_3d_dicom.py             | 4 ++--
 4 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index f59f938..84190e0 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -78,3 +78,5 @@ jobs:
         pip install setuptools wheel
         pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ nii2dcm==$NII2DCM_VERSION
         nii2dcm -h
+        echo "nii2dcm version:"
+        nii2dcm -v
diff --git a/nii2dcm/modules/image_pixel.py b/nii2dcm/modules/image_pixel.py
index 4e94052..bf91e29 100644
--- a/nii2dcm/modules/image_pixel.py
+++ b/nii2dcm/modules/image_pixel.py
@@ -29,14 +29,14 @@ def __init__(self):
         self.ds.BitsAllocated = 1
         self.ds.BitsStored = ''
         self.ds.HighBit = ''
-    
+
         # PixelRepresentation
         # Enumerated values either: unsigned integer or two's complement
         # Setting = 0, as observed in real DICOM
         self.ds.PixelRepresentation = 0
-    
+
         self.ds.SmallestImagePixelValue = ''
         self.ds.LargestImagePixelValue = ''
-    
+
         # PixelData written in dcm_writer via Pydicom
         self.ds.PixelData = ''
diff --git a/nii2dcm/nii.py b/nii2dcm/nii.py
index a7ab1e8..7aa11ca 100644
--- a/nii2dcm/nii.py
+++ b/nii2dcm/nii.py
@@ -39,7 +39,7 @@ def fnT1N(A, N):
         sliceIndices = np.repeat(range(1, nZ+1), nF)
         voxelSpacing = dimZ
         zLocLast = (voxelSpacing * nZ) - voxelSpacing
-        sliceLoca = np.repeat( np.linspace(0, zLocLast, num=nZ), nF)
+        sliceLoca = np.repeat(np.linspace(0, zLocLast, num=nZ), nF)
 
         # Windowing & Signal Intensity
         maxI = np.amax(nii_img)
diff --git a/scripts/create_3d_dicom.py b/scripts/create_3d_dicom.py
index c742db9..1814162 100644
--- a/scripts/create_3d_dicom.py
+++ b/scripts/create_3d_dicom.py
@@ -14,8 +14,8 @@
 
 
 NII2DCM_DIR = r'/Users/tr17/code/nii2dcm'
-INPUT_DIR   = r'/Users/tr17/code/nii2dcm/input/'
-OUTPUT_DIR  = r'/Users/tr17/code/nii2dcm/output'
+INPUT_DIR = r'/Users/tr17/code/nii2dcm/input/'
+OUTPUT_DIR = r'/Users/tr17/code/nii2dcm/output'
 
 if not os.path.isdir(OUTPUT_DIR):
     os.makedirs(OUTPUT_DIR)

From eba4901e93b021e68dca391e30a90ad889c8620b Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:43:03 +0100
Subject: [PATCH 36/37] Increase wait time for TestPyPI to update

---
 .github/workflows/publish_testpypi.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 84190e0..6387e14 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -66,7 +66,7 @@ jobs:
     - name: Wait to allow TestPyPI to update
       uses: GuillaumeFalourd/wait-sleep-action@v1
       with:
-        time: '1m'
+        time: '90'  # seconds
 
     - name: Install latest TestPyPI version in fresh venv
       run: |

From 2d728806e49ab2d4bf4a59063895256e837adaf0 Mon Sep 17 00:00:00 2001
From: Tom Roberts <t.roberts@kcl.ac.uk>
Date: Thu, 24 Aug 2023 16:51:07 +0100
Subject: [PATCH 37/37] Increase TestPyPI wait time to 2.5 mins

---
 .github/workflows/publish_testpypi.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish_testpypi.yml b/.github/workflows/publish_testpypi.yml
index 6387e14..79b4420 100644
--- a/.github/workflows/publish_testpypi.yml
+++ b/.github/workflows/publish_testpypi.yml
@@ -66,7 +66,7 @@ jobs:
     - name: Wait to allow TestPyPI to update
       uses: GuillaumeFalourd/wait-sleep-action@v1
       with:
-        time: '90'  # seconds
+        time: '150'  # seconds
 
     - name: Install latest TestPyPI version in fresh venv
       run: |