From 66f3989a37d57da0044c59d79e24bc20c347c418 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 10:01:03 +0200
Subject: [PATCH 01/18] [ENH]: added installation instructions and metadata in
 a pyproject.toml file

---
 pyproject.toml | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 pyproject.toml

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..bd3d52a
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "shanoir-downloader"
+version = "0.0.1"
+dynamic = ["version"]
+dynamic = ["dependencies", "optional-dependencies"]
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
+optional-dependencies = {dev = { file = ["requirements-dev.txt"] }}
+
+requires-python = ">=3.8 <3.12"
+
+authors = [
+  {name = "Arthur Masson"},
+  {name = "Quentin Duché"},
+  {name = "Malo Gaubert"},
+]
+maintainers = [
+  {name = "Quentin Duché", email = "quentin.duche@inria.fr"}
+]
+description = "Download Shanoir Datasets in various format using Python"
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = ["Shanoir", "DICOM", "NIFTI", "BIDS"]
+classifiers = [
+  "Programming Language :: Python"
+]
+
+[project.urls]
+Repository = "https://github.com/Inria-Empenn/shanoir_downloader.git"
+"Bug Tracker" = "https://github.com/Inria-Empenn/shanoir_downloader/issues"
+Changelog = "https://github.com/Inria-Empenn/shanoir_downloader/blob/master/CHANGELOG.md"
+
+[project.scripts]
+spam-cli = "shanoir-downloader:main_cli"
+
+
+[project.entry-points."spam.magical"]
+tomatoes = "spam:main_tomatoes"
\ No newline at end of file

From 5b8367baf44e1dededf7e25d7880b40c68f593b1 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 10:47:25 +0200
Subject: [PATCH 02/18] [ENH]: fixed dependencies and build backend issue

---
 pyproject.toml | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index bd3d52a..37a6d78 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,14 +5,10 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "shanoir-downloader"
 version = "0.0.1"
-dynamic = ["version"]
-dynamic = ["dependencies", "optional-dependencies"]
 
-[tool.setuptools.dynamic]
-dependencies = {file = ["requirements.txt"]}
-optional-dependencies = {dev = { file = ["requirements-dev.txt"] }}
+dynamic = ["dependencies", "optional-dependencies"]
 
-requires-python = ">=3.8 <3.12"
+requires-python = ">=3.8, <3.12"
 
 authors = [
   {name = "Arthur Masson"},
@@ -35,9 +31,16 @@ Repository = "https://github.com/Inria-Empenn/shanoir_downloader.git"
 "Bug Tracker" = "https://github.com/Inria-Empenn/shanoir_downloader/issues"
 Changelog = "https://github.com/Inria-Empenn/shanoir_downloader/blob/master/CHANGELOG.md"
 
-[project.scripts]
-spam-cli = "shanoir-downloader:main_cli"
+[tool.setuptools]
+py-modules = []
+
+[tool.setuptools.dynamic]
+dependencies = {file = ["requirements.txt"]}
 
+#optional-dependencies = {dev = { file = ["requirements-dev.txt"] }}
+#[project.scripts]
+#spam-cli = "shanoir-downloader:main_cli"
 
-[project.entry-points."spam.magical"]
-tomatoes = "spam:main_tomatoes"
\ No newline at end of file
+#
+#[project.entry-points."spam.magical"]
+#tomatoes = "spam:main_tomatoes"
\ No newline at end of file

From 2525fe98758ee2385d83ed0ee274d059d58cc5da Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 10:47:40 +0200
Subject: [PATCH 03/18] [ENH]: fixed dependencies and build backend issue

---
 Readme.md => README.md | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename Readme.md => README.md (100%)

diff --git a/Readme.md b/README.md
similarity index 100%
rename from Readme.md
rename to README.md

From f3c572317438f8a28498a7fa462b71b001447df6 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 10:51:47 +0200
Subject: [PATCH 04/18] [ENH]: added authors emails

---
 pyproject.toml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 37a6d78..5f8e986 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,12 +11,12 @@ dynamic = ["dependencies", "optional-dependencies"]
 requires-python = ">=3.8, <3.12"
 
 authors = [
-  {name = "Arthur Masson"},
-  {name = "Quentin Duché"},
-  {name = "Malo Gaubert"},
+  {name = "Arthur Masson",email = "arthur.masson@inria.fr"},
+  {name = "Quentin Duché", email = "quentin.duche@irisa.fr"},
+  {name = "Malo Gaubert", email = "malo.gaubert@irisa.fr"},
 ]
 maintainers = [
-  {name = "Quentin Duché", email = "quentin.duche@inria.fr"}
+  {name = "Quentin Duché", email = "quentin.duche@irisa.fr"}
 ]
 description = "Download Shanoir Datasets in various format using Python"
 readme = "README.md"

From a9f76fb0ed7d5761d0e367eb4b628ecbce1c1533 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 10:53:40 +0200
Subject: [PATCH 05/18] [ENH]: adapted installations instructions in the README
 to new mechanism

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

diff --git a/README.md b/README.md
index 0c2ea88..779f271 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@ The scripts `convert_dicoms_to_niftis.py` and `create_previews.py` enable to con
 
 It is advised to install the project in [a virtual environment](https://docs.python.org/3/tutorial/venv.html). 
 
-[Install python with pip](https://www.python.org/downloads/) ; then use `pip install -r requirements.txt` to install python dependencies.
+[Install python with pip](https://www.python.org/downloads/) ; then use `pip install .` to install python dependencies.
 
 Optionally, rename the `.env.example` to `.env` and set the variables (`shanoir_password`, `gpg_recipient`) to your needs.
 

From dec799ddcacfdd2a0264c51b7f5bfc0044484346 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 11:27:12 +0200
Subject: [PATCH 06/18] [ENH]: added CI to test shanoir downloader basic
 installation

---
 .github/workflows/python-installation.yml | 36 +++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 .github/workflows/python-installation.yml

diff --git a/.github/workflows/python-installation.yml b/.github/workflows/python-installation.yml
new file mode 100644
index 0000000..8263f98
--- /dev/null
+++ b/.github/workflows/python-installation.yml
@@ -0,0 +1,36 @@
+name: Python installation
+
+on: [push]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        #TODO: use github action to read python version from pyproject.toml
+    runs-on:  ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python # Set Python version
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      # Create virtual env under each python version
+      # (optional and a bit redundant because we are already on a specific python)
+      # it insures installation instruction provided in README are working
+      - name: Install dependencies
+        run: |
+          python -m venv test-env --clear
+          source test-env/bin/activate
+          python -m pip install --upgrade pip
+          python -m pip install -e .
+#      - name: Test with pytest
+#        run: pytest tests.py --doctest-modules --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+#      - name: Upload pytest test results
+#        uses: actions/upload-artifact@v4
+#        with:
+#          name: pytest-results-${{ matrix.python-version }}
+#          path: junit/test-results-${{ matrix.python-version }}.xml
+#        # Use always() to always run this step to publish test results when there are test failures
+#        if: ${{ always() }}

From 582a005d4e7fbc55998e3c905ba17035c7239756 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 11:40:40 +0200
Subject: [PATCH 07/18] [ENH]: restrained to ubuntu in the first time

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

diff --git a/.github/workflows/python-installation.yml b/.github/workflows/python-installation.yml
index 8263f98..da42404 100644
--- a/.github/workflows/python-installation.yml
+++ b/.github/workflows/python-installation.yml
@@ -6,7 +6,7 @@ jobs:
   build:
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
         python-version: ["3.8", "3.9", "3.10", "3.11"]
         #TODO: use github action to read python version from pyproject.toml
     runs-on:  ${{ matrix.os }}

From f0e9a716b23752bd010672bee1365a53daa68731 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 11:53:04 +0200
Subject: [PATCH 08/18] [BF]: try fix bug with python 3.11 installation

---
 pyproject.toml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5f8e986..909ff39 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools"]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -34,9 +34,13 @@ Changelog = "https://github.com/Inria-Empenn/shanoir_downloader/blob/master/CHAN
 [tool.setuptools]
 py-modules = []
 
+[tool.setuptools_scm]
+version_file = "pkg/_version.py"
+
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}
 
+
 #optional-dependencies = {dev = { file = ["requirements-dev.txt"] }}
 #[project.scripts]
 #spam-cli = "shanoir-downloader:main_cli"

From d54e6b3d549d8d4cf7804c2c1680904dae4e3df9 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 11:54:26 +0200
Subject: [PATCH 09/18] [BF]: fix syntax

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

diff --git a/pyproject.toml b/pyproject.toml
index 909ff39..af25598 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,7 +35,7 @@ Changelog = "https://github.com/Inria-Empenn/shanoir_downloader/blob/master/CHAN
 py-modules = []
 
 [tool.setuptools_scm]
-version_file = "pkg/_version.py"
+
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}

From 784718c23ba7bd285ca98ec1109891c485d93520 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Tue, 16 Jul 2024 12:03:51 +0200
Subject: [PATCH 10/18] [BF]: restrained python version to python<3.11

---
 .github/workflows/python-installation.yml | 2 +-
 pyproject.toml                            | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/python-installation.yml b/.github/workflows/python-installation.yml
index da42404..47530d9 100644
--- a/.github/workflows/python-installation.yml
+++ b/.github/workflows/python-installation.yml
@@ -7,7 +7,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10"]
         #TODO: use github action to read python version from pyproject.toml
     runs-on:  ${{ matrix.os }}
     steps:
diff --git a/pyproject.toml b/pyproject.toml
index af25598..9ce4885 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ version = "0.0.1"
 
 dynamic = ["dependencies", "optional-dependencies"]
 
-requires-python = ">=3.8, <3.12"
+requires-python = ">=3.8, <3.11"
 
 authors = [
   {name = "Arthur Masson",email = "arthur.masson@inria.fr"},
@@ -36,7 +36,6 @@ py-modules = []
 
 [tool.setuptools_scm]
 
-
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements.txt"]}
 

From 147e3ac283f43b82c3cb55cbddc7467812cdfd63 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Thu, 18 Jul 2024 15:11:52 +0200
Subject: [PATCH 11/18] [BF]: added environment.yml corresponding to
 requirements.txt

---
 environment.yml | 208 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 208 insertions(+)
 create mode 100644 environment.yml

diff --git a/environment.yml b/environment.yml
new file mode 100644
index 0000000..2465de7
--- /dev/null
+++ b/environment.yml
@@ -0,0 +1,208 @@
+name: test-install
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=2_gnu
+  - annexremote=1.6.5=py310hff52083_0
+  - atk-1.0=2.36.0=h516909a_2
+  - backports=1.0=pyhd8ed1ab_3
+  - backports.tarfile=1.0.0=pyhd8ed1ab_1
+  - boto3=1.34.144=pyhd8ed1ab_0
+  - botocore=1.34.144=pyge310_1234567_0
+  - brotli=1.1.0=hd590300_1
+  - brotli-bin=1.1.0=hd590300_1
+  - brotli-python=1.0.9=py310hd8f1fbe_7
+  - bz2file=0.98=py_0
+  - bzip2=1.0.8=h5eee18b_6
+  - c-ares=1.32.2=h4bc722e_0
+  - ca-certificates=2024.7.4=hbcca054_0
+  - cached-property=1.5.2=hd8ed1ab_1
+  - cached_property=1.5.2=pyha770c72_1
+  - cairo=1.16.0=hb05425b_5
+  - cffi=1.16.0=py310h2fee648_0
+  - chardet=5.2.0=py310hff52083_1
+  - ci-info=0.3.0=pyhd8ed1ab_0
+  - click=8.1.7=unix_pyh707e725_0
+  - colorama=0.4.6=pyhd8ed1ab_0
+  - cryptography=42.0.8=py310hb1bd9d3_0
+  - curl=8.7.1=hdbd6064_0
+  - cycler=0.12.1=pyhd8ed1ab_0
+  - datalad=1.1.1=py310hff52083_0
+  - dbus=1.13.6=he372182_0
+  - dcm2niix=1.0.20211006=h4bd325d_0
+  - dcmstack=0.8.0=pyhd8ed1ab_3
+  - distro=1.9.0=pyhd8ed1ab_0
+  - etelemetry=0.3.1=pyhd8ed1ab_0
+  - exifread=3.0.0=pyhd8ed1ab_0
+  - expat=2.6.2=h59595ed_0
+  - fasteners=0.17.3=pyhd8ed1ab_0
+  - filelock=3.15.4=pyhd8ed1ab_0
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=h77eed37_2
+  - fontconfig=2.14.1=h4c34cd2_2
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - fonttools=4.53.1=py310h5b4e0ec_0
+  - freetype=2.10.4=h0708190_1
+  - fribidi=1.0.10=h36c2ea0_0
+  - gdk-pixbuf=2.42.10=h5eee18b_0
+  - gettext=0.21.1=h27087fc_0
+  - git=2.33.0=pl5321hf874766_1
+  - git-annex=10.20230626=nodep_h1234567_1
+  - glib=2.69.1=he621ea3_2
+  - gobject-introspection=1.72.0=py310hbb6d50b_2
+  - graphite2=1.3.14=h295c915_1
+  - graphviz=2.50.0=h3cd0ef9_0
+  - gtk2=2.24.33=h73c1081_2
+  - gts=0.7.6=h08bb679_0
+  - h2=4.1.0=pyhd8ed1ab_0
+  - h5py=3.7.0=nompi_py310h06dffec_100
+  - harfbuzz=4.3.0=hf52aaf7_2
+  - hdf5=1.12.1=h2b7332f_3
+  - heudiconv=1.1.6=pyhd8ed1ab_0
+  - hpack=4.0.0=pyh9f0ad1d_0
+  - humanize=4.10.0=pyhd8ed1ab_0
+  - hyperframe=6.0.1=pyhd8ed1ab_0
+  - icu=73.1=h6a678d5_0
+  - importlib_metadata=8.0.0=hd8ed1ab_0
+  - importlib_resources=6.4.0=pyhd8ed1ab_0
+  - iso8601=2.1.0=pyhd8ed1ab_0
+  - isodate=0.6.1=pyhd8ed1ab_0
+  - jaraco.classes=3.4.0=pyhd8ed1ab_1
+  - jaraco.context=5.3.0=pyhd8ed1ab_1
+  - jaraco.functools=4.0.0=pyhd8ed1ab_0
+  - jeepney=0.8.0=pyhd8ed1ab_0
+  - jmespath=1.0.1=pyhd8ed1ab_0
+  - jpeg=9e=h0b41bf4_3
+  - keyring=25.2.1=pyha804496_0
+  - keyrings.alt=5.0.1=pyhd8ed1ab_1
+  - kiwisolver=1.4.2=py310hbf28c38_1
+  - krb5=1.20.1=h143b758_1
+  - lcms2=2.15=hfd0df8a_0
+  - ld_impl_linux-64=2.38=h1181459_1
+  - lerc=3.0=h9c3ff4c_0
+  - libblas=3.9.0=20_linux64_openblas
+  - libbrotlicommon=1.1.0=hd590300_1
+  - libbrotlidec=1.1.0=hd590300_1
+  - libbrotlienc=1.1.0=hd590300_1
+  - libcblas=3.9.0=20_linux64_openblas
+  - libcurl=8.7.1=h251f7ec_0
+  - libdeflate=1.17=h0b41bf4_0
+  - libedit=3.1.20230828=h5eee18b_0
+  - libev=4.33=hd590300_2
+  - libexpat=2.6.2=h59595ed_0
+  - libffi=3.4.4=h6a678d5_1
+  - libgcc-ng=14.1.0=h77fa898_0
+  - libgd=2.3.3=h695aa2c_1
+  - libgfortran-ng=14.1.0=h69a702a_0
+  - libgfortran5=14.1.0=hc5f4f2c_0
+  - libgomp=14.1.0=h77fa898_0
+  - libiconv=1.17=hd590300_2
+  - liblapack=3.9.0=20_linux64_openblas
+  - libnghttp2=1.57.0=h2d74bed_0
+  - libopenblas=0.3.25=pthreads_h413a1c8_0
+  - libpng=1.6.39=h5eee18b_0
+  - librsvg=2.54.4=h36cc946_3
+  - libssh2=1.10.0=ha35d2d1_2
+  - libstdcxx-ng=11.2.0=h1234567_1
+  - libtiff=4.5.1=h6a678d5_0
+  - libtool=2.4.7=h27087fc_0
+  - libuuid=1.41.5=h5eee18b_0
+  - libwebp-base=1.4.0=hd590300_0
+  - libxcb=1.16=hd590300_0
+  - libxcrypt=4.4.36=hd590300_1
+  - libxml2=2.10.4=hfdd30dd_2
+  - libxslt=1.1.37=h873f0b0_0
+  - looseversion=1.3.0=pyhd8ed1ab_0
+  - lxml=4.9.1=py310h5764c6d_0
+  - lz4-c=1.9.4=h6a678d5_1
+  - matplotlib-base=3.5.2=py310h5701ce4_0
+  - more-itertools=10.3.0=pyhd8ed1ab_0
+  - msgpack-python=1.0.3=py310hbf28c38_1
+  - munkres=1.1.4=pyh9f0ad1d_0
+  - mutagen=1.47.0=pyhd8ed1ab_0
+  - ncurses=6.4=h6a678d5_0
+  - networkx=3.2=pyhd8ed1ab_0
+  - nipype=1.8.6=py310hff52083_0
+  - numpy=1.22.3=py310h4ef5377_2
+  - openjpeg=2.4.0=h9ca470c_2
+  - openssl=3.3.1=h4bc722e_2
+  - p7zip=16.02=h9c3ff4c_1001
+  - packaging=24.1=pyhd8ed1ab_0
+  - pango=1.50.7=h05da053_0
+  - pathlib=1.0.1=py310hff52083_7
+  - patool=2.3.0=pyhd8ed1ab_0
+  - pcre=8.45=h9c3ff4c_0
+  - pcre2=10.37=h032f7d1_0
+  - perl=5.32.1=7_hd590300_perl5
+  - pip=24.0=py310h06a4308_0
+  - pixman=0.40.0=h36c2ea0_0
+  - platformdirs=4.2.2=pyhd8ed1ab_0
+  - prov=2.0.0=pyhd3deb0d_0
+  - psutil=6.0.0=py310hc51659f_0
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - pycparser=2.22=pyhd8ed1ab_0
+  - pydot=3.0.1=py310hff52083_0
+  - pyparsing=3.1.2=pyhd8ed1ab_0
+  - pyperclip=1.8.2=pyhd8ed1ab_2
+  - pysocks=1.7.1=pyha2e5f31_6
+  - python=3.10.14=h955ad1f_1
+  - python-gitlab=4.8.0=pyhd8ed1ab_0
+  - python_abi=3.10=2_cp310
+  - rdflib=7.0.0=pyhd8ed1ab_0
+  - readline=8.2=h5eee18b_0
+  - requests-ftp=0.3.1=py_1
+  - requests-toolbelt=1.0.0=pyhd8ed1ab_0
+  - s3transfer=0.10.2=pyhd8ed1ab_0
+  - secretstorage=3.3.3=py310hff52083_2
+  - setuptools=69.5.1=py310h06a4308_0
+  - simplejson=3.19.2=py310h2372a71_0
+  - six=1.16.0=pyh6c4a22f_0
+  - sqlite=3.45.3=h5eee18b_0
+  - tk=8.6.14=h39e8969_0
+  - traits=6.3.2=py310h5764c6d_1
+  - typing_extensions=4.12.2=pyha770c72_0
+  - tzdata=2024a=h04d1e81_0
+  - unicodedata2=15.1.0=py310h2372a71_0
+  - wheel=0.43.0=py310h06a4308_0
+  - whoosh=2.7.4=py310hff52083_8
+  - xorg-libxau=1.0.11=hd590300_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xvfbwrapper=0.2.9=pyhd8ed1ab_1005
+  - xz=5.4.6=h5eee18b_1
+  - zlib=1.2.13=h5eee18b_1
+  - zstandard=0.22.0=py310h1275a96_0
+  - zstd=1.5.5=hc292b87_2
+  - pip:
+      - certifi==2021.10.8
+      - charset-normalizer==2.0.8
+      - dicom2nifti==2.3.0
+      - dicomanonymizer==0.0.1
+      - idna==3.3
+      - importlib-metadata==4.8.2
+      - multivolumefile==0.2.3
+      - nibabel==5.2.1
+      - pandas==1.4.2
+      - pillow==9.0.0
+      - py7zr==0.17.0
+      - pybcj==0.5.0
+      - pycryptodomex==3.12.0
+      - pydicom==2.2.2
+      - pyppmd==0.17.3
+      - python-dateutil==2.8.2
+      - python-dotenv==0.19.2
+      - pytz==2021.3
+      - pyzstd==0.15.0
+      - requests==2.26.0
+      - scipy==1.11.4
+      - simpleitk==2.1.1.2
+      - texttable==1.6.4
+      - tqdm==4.62.3
+      - typing-extensions==4.0.1
+      - urllib3==1.26.7
+      - zipp==3.6.0
+prefix: /home/alpron/softs/miniconda3/envs/test

From 736e320b5264c4f5ffd1abf9061957f39a8ab49f Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Thu, 18 Jul 2024 15:22:37 +0200
Subject: [PATCH 12/18] [BF]: fix pip and conda installation syntax

---
 .github/workflows/conda-installation.yml      | 34 +++++++++++++++++++
 ...-installation.yml => pip-installation.yml} |  0
 2 files changed, 34 insertions(+)
 create mode 100644 .github/workflows/conda-installation.yml
 rename .github/workflows/{python-installation.yml => pip-installation.yml} (100%)

diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml
new file mode 100644
index 0000000..132af25
--- /dev/null
+++ b/.github/workflows/conda-installation.yml
@@ -0,0 +1,34 @@
+name: Python installation
+
+on: [push]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.8", "3.9", "3.10"]
+        #TODO: use github action to read python version from pyproject.toml
+    runs-on:  ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Python
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          environment-file: environment.yml
+          activate-environment: test-install
+          python-version: ${{ matrix.python-version }}
+
+      # Create virtual env under each python version
+      # (optional and a bit redundant because we are already on a specific python)
+      # it insures installation instruction provided in README are working
+#      - name: Test with pytest
+#        run: pytest tests.py --doctest-modules --junitxml=junit/test-results-${{ matrix.python-version }}.xml
+#      - name: Upload pytest test results
+#        uses: actions/upload-artifact@v4
+#        with:
+#          name: pytest-results-${{ matrix.python-version }}
+#          path: junit/test-results-${{ matrix.python-version }}.xml
+#        # Use always() to always run this step to publish test results when there are test failures
+#        if: ${{ always() }}
diff --git a/.github/workflows/python-installation.yml b/.github/workflows/pip-installation.yml
similarity index 100%
rename from .github/workflows/python-installation.yml
rename to .github/workflows/pip-installation.yml

From f9a438a546a0fb1baaf14e3b75e80365e0bbd932 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Thu, 18 Jul 2024 15:34:16 +0200
Subject: [PATCH 13/18] [BF]: fix pip and conda installation syntax

---
 .github/workflows/conda-installation.yml | 2 +-
 .github/workflows/pip-installation.yml   | 4 ++--
 README.md                                | 9 +++++++--
 environment.yml                          | 2 +-
 4 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml
index 132af25..d8becbc 100644
--- a/.github/workflows/conda-installation.yml
+++ b/.github/workflows/conda-installation.yml
@@ -17,7 +17,7 @@ jobs:
         with:
           auto-update-conda: true
           environment-file: environment.yml
-          activate-environment: test-install
+          activate-environment: working-env
           python-version: ${{ matrix.python-version }}
 
       # Create virtual env under each python version
diff --git a/.github/workflows/pip-installation.yml b/.github/workflows/pip-installation.yml
index 47530d9..50c97b9 100644
--- a/.github/workflows/pip-installation.yml
+++ b/.github/workflows/pip-installation.yml
@@ -21,8 +21,8 @@ jobs:
       # it insures installation instruction provided in README are working
       - name: Install dependencies
         run: |
-          python -m venv test-env --clear
-          source test-env/bin/activate
+          python -m venv working-env --clear
+          source working-env/bin/activate
           python -m pip install --upgrade pip
           python -m pip install -e .
 #      - name: Test with pytest
diff --git a/README.md b/README.md
index 779f271..e0c44ab 100644
--- a/README.md
+++ b/README.md
@@ -8,14 +8,19 @@ The scripts `convert_dicoms_to_niftis.py` and `create_previews.py` enable to con
 
 ## Install
 
-It is advised to install the project in [a virtual environment](https://docs.python.org/3/tutorial/venv.html). 
-
+It is advised to install the project in python virtual environment relying either on [venv](https://docs.python.org/3/tutorial/venv.html) or preferably  [(mini)conda](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
+### Installation with pip 
 [Install python with pip](https://www.python.org/downloads/) ; then use `pip install .` to install python dependencies.
 
 Optionally, rename the `.env.example` to `.env` and set the variables (`shanoir_password`, `gpg_recipient`) to your needs.
 
 *See the "Installing DicomAnonymizer" section if you want to use DicomAnonymizer for the dicom anonymization instead of PyDicom.*
 
+### Installation with conda
+> [!IMPORTANT]
+> This installation is required if shanoir2bids.py is used 
+
+After installing a (mini)conda distribution type in a terminal  `conda create -f environment.yml` then activate the environment using `conda activate working-env` where `working-env` is the default name of the created environment 
 ## Usage
 
 There are three scripts to download datasets:
diff --git a/environment.yml b/environment.yml
index 2465de7..7a0d5fd 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,4 +1,4 @@
-name: test-install
+name: working-env
 channels:
   - conda-forge
   - defaults

From 4b13f024e79646b742941954a2f7dbb1f70943c6 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Thu, 18 Jul 2024 16:28:41 +0200
Subject: [PATCH 14/18] [BF]: fix pip and conda installation syntax

---
 .github/workflows/conda-installation.yml |   5 +-
 environment.yml                          | 208 -----------------------
 2 files changed, 4 insertions(+), 209 deletions(-)
 delete mode 100644 environment.yml

diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml
index d8becbc..198d557 100644
--- a/.github/workflows/conda-installation.yml
+++ b/.github/workflows/conda-installation.yml
@@ -16,9 +16,12 @@ jobs:
         uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
-          environment-file: environment.yml
           activate-environment: working-env
           python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install -e .
+          conda install -c conda-forge heudiconv git-annex=*alldep datalaad
 
       # Create virtual env under each python version
       # (optional and a bit redundant because we are already on a specific python)
diff --git a/environment.yml b/environment.yml
deleted file mode 100644
index 7a0d5fd..0000000
--- a/environment.yml
+++ /dev/null
@@ -1,208 +0,0 @@
-name: working-env
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - _libgcc_mutex=0.1=conda_forge
-  - _openmp_mutex=4.5=2_gnu
-  - annexremote=1.6.5=py310hff52083_0
-  - atk-1.0=2.36.0=h516909a_2
-  - backports=1.0=pyhd8ed1ab_3
-  - backports.tarfile=1.0.0=pyhd8ed1ab_1
-  - boto3=1.34.144=pyhd8ed1ab_0
-  - botocore=1.34.144=pyge310_1234567_0
-  - brotli=1.1.0=hd590300_1
-  - brotli-bin=1.1.0=hd590300_1
-  - brotli-python=1.0.9=py310hd8f1fbe_7
-  - bz2file=0.98=py_0
-  - bzip2=1.0.8=h5eee18b_6
-  - c-ares=1.32.2=h4bc722e_0
-  - ca-certificates=2024.7.4=hbcca054_0
-  - cached-property=1.5.2=hd8ed1ab_1
-  - cached_property=1.5.2=pyha770c72_1
-  - cairo=1.16.0=hb05425b_5
-  - cffi=1.16.0=py310h2fee648_0
-  - chardet=5.2.0=py310hff52083_1
-  - ci-info=0.3.0=pyhd8ed1ab_0
-  - click=8.1.7=unix_pyh707e725_0
-  - colorama=0.4.6=pyhd8ed1ab_0
-  - cryptography=42.0.8=py310hb1bd9d3_0
-  - curl=8.7.1=hdbd6064_0
-  - cycler=0.12.1=pyhd8ed1ab_0
-  - datalad=1.1.1=py310hff52083_0
-  - dbus=1.13.6=he372182_0
-  - dcm2niix=1.0.20211006=h4bd325d_0
-  - dcmstack=0.8.0=pyhd8ed1ab_3
-  - distro=1.9.0=pyhd8ed1ab_0
-  - etelemetry=0.3.1=pyhd8ed1ab_0
-  - exifread=3.0.0=pyhd8ed1ab_0
-  - expat=2.6.2=h59595ed_0
-  - fasteners=0.17.3=pyhd8ed1ab_0
-  - filelock=3.15.4=pyhd8ed1ab_0
-  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
-  - font-ttf-inconsolata=3.000=h77eed37_0
-  - font-ttf-source-code-pro=2.038=h77eed37_0
-  - font-ttf-ubuntu=0.83=h77eed37_2
-  - fontconfig=2.14.1=h4c34cd2_2
-  - fonts-conda-ecosystem=1=0
-  - fonts-conda-forge=1=0
-  - fonttools=4.53.1=py310h5b4e0ec_0
-  - freetype=2.10.4=h0708190_1
-  - fribidi=1.0.10=h36c2ea0_0
-  - gdk-pixbuf=2.42.10=h5eee18b_0
-  - gettext=0.21.1=h27087fc_0
-  - git=2.33.0=pl5321hf874766_1
-  - git-annex=10.20230626=nodep_h1234567_1
-  - glib=2.69.1=he621ea3_2
-  - gobject-introspection=1.72.0=py310hbb6d50b_2
-  - graphite2=1.3.14=h295c915_1
-  - graphviz=2.50.0=h3cd0ef9_0
-  - gtk2=2.24.33=h73c1081_2
-  - gts=0.7.6=h08bb679_0
-  - h2=4.1.0=pyhd8ed1ab_0
-  - h5py=3.7.0=nompi_py310h06dffec_100
-  - harfbuzz=4.3.0=hf52aaf7_2
-  - hdf5=1.12.1=h2b7332f_3
-  - heudiconv=1.1.6=pyhd8ed1ab_0
-  - hpack=4.0.0=pyh9f0ad1d_0
-  - humanize=4.10.0=pyhd8ed1ab_0
-  - hyperframe=6.0.1=pyhd8ed1ab_0
-  - icu=73.1=h6a678d5_0
-  - importlib_metadata=8.0.0=hd8ed1ab_0
-  - importlib_resources=6.4.0=pyhd8ed1ab_0
-  - iso8601=2.1.0=pyhd8ed1ab_0
-  - isodate=0.6.1=pyhd8ed1ab_0
-  - jaraco.classes=3.4.0=pyhd8ed1ab_1
-  - jaraco.context=5.3.0=pyhd8ed1ab_1
-  - jaraco.functools=4.0.0=pyhd8ed1ab_0
-  - jeepney=0.8.0=pyhd8ed1ab_0
-  - jmespath=1.0.1=pyhd8ed1ab_0
-  - jpeg=9e=h0b41bf4_3
-  - keyring=25.2.1=pyha804496_0
-  - keyrings.alt=5.0.1=pyhd8ed1ab_1
-  - kiwisolver=1.4.2=py310hbf28c38_1
-  - krb5=1.20.1=h143b758_1
-  - lcms2=2.15=hfd0df8a_0
-  - ld_impl_linux-64=2.38=h1181459_1
-  - lerc=3.0=h9c3ff4c_0
-  - libblas=3.9.0=20_linux64_openblas
-  - libbrotlicommon=1.1.0=hd590300_1
-  - libbrotlidec=1.1.0=hd590300_1
-  - libbrotlienc=1.1.0=hd590300_1
-  - libcblas=3.9.0=20_linux64_openblas
-  - libcurl=8.7.1=h251f7ec_0
-  - libdeflate=1.17=h0b41bf4_0
-  - libedit=3.1.20230828=h5eee18b_0
-  - libev=4.33=hd590300_2
-  - libexpat=2.6.2=h59595ed_0
-  - libffi=3.4.4=h6a678d5_1
-  - libgcc-ng=14.1.0=h77fa898_0
-  - libgd=2.3.3=h695aa2c_1
-  - libgfortran-ng=14.1.0=h69a702a_0
-  - libgfortran5=14.1.0=hc5f4f2c_0
-  - libgomp=14.1.0=h77fa898_0
-  - libiconv=1.17=hd590300_2
-  - liblapack=3.9.0=20_linux64_openblas
-  - libnghttp2=1.57.0=h2d74bed_0
-  - libopenblas=0.3.25=pthreads_h413a1c8_0
-  - libpng=1.6.39=h5eee18b_0
-  - librsvg=2.54.4=h36cc946_3
-  - libssh2=1.10.0=ha35d2d1_2
-  - libstdcxx-ng=11.2.0=h1234567_1
-  - libtiff=4.5.1=h6a678d5_0
-  - libtool=2.4.7=h27087fc_0
-  - libuuid=1.41.5=h5eee18b_0
-  - libwebp-base=1.4.0=hd590300_0
-  - libxcb=1.16=hd590300_0
-  - libxcrypt=4.4.36=hd590300_1
-  - libxml2=2.10.4=hfdd30dd_2
-  - libxslt=1.1.37=h873f0b0_0
-  - looseversion=1.3.0=pyhd8ed1ab_0
-  - lxml=4.9.1=py310h5764c6d_0
-  - lz4-c=1.9.4=h6a678d5_1
-  - matplotlib-base=3.5.2=py310h5701ce4_0
-  - more-itertools=10.3.0=pyhd8ed1ab_0
-  - msgpack-python=1.0.3=py310hbf28c38_1
-  - munkres=1.1.4=pyh9f0ad1d_0
-  - mutagen=1.47.0=pyhd8ed1ab_0
-  - ncurses=6.4=h6a678d5_0
-  - networkx=3.2=pyhd8ed1ab_0
-  - nipype=1.8.6=py310hff52083_0
-  - numpy=1.22.3=py310h4ef5377_2
-  - openjpeg=2.4.0=h9ca470c_2
-  - openssl=3.3.1=h4bc722e_2
-  - p7zip=16.02=h9c3ff4c_1001
-  - packaging=24.1=pyhd8ed1ab_0
-  - pango=1.50.7=h05da053_0
-  - pathlib=1.0.1=py310hff52083_7
-  - patool=2.3.0=pyhd8ed1ab_0
-  - pcre=8.45=h9c3ff4c_0
-  - pcre2=10.37=h032f7d1_0
-  - perl=5.32.1=7_hd590300_perl5
-  - pip=24.0=py310h06a4308_0
-  - pixman=0.40.0=h36c2ea0_0
-  - platformdirs=4.2.2=pyhd8ed1ab_0
-  - prov=2.0.0=pyhd3deb0d_0
-  - psutil=6.0.0=py310hc51659f_0
-  - pthread-stubs=0.4=h36c2ea0_1001
-  - pycparser=2.22=pyhd8ed1ab_0
-  - pydot=3.0.1=py310hff52083_0
-  - pyparsing=3.1.2=pyhd8ed1ab_0
-  - pyperclip=1.8.2=pyhd8ed1ab_2
-  - pysocks=1.7.1=pyha2e5f31_6
-  - python=3.10.14=h955ad1f_1
-  - python-gitlab=4.8.0=pyhd8ed1ab_0
-  - python_abi=3.10=2_cp310
-  - rdflib=7.0.0=pyhd8ed1ab_0
-  - readline=8.2=h5eee18b_0
-  - requests-ftp=0.3.1=py_1
-  - requests-toolbelt=1.0.0=pyhd8ed1ab_0
-  - s3transfer=0.10.2=pyhd8ed1ab_0
-  - secretstorage=3.3.3=py310hff52083_2
-  - setuptools=69.5.1=py310h06a4308_0
-  - simplejson=3.19.2=py310h2372a71_0
-  - six=1.16.0=pyh6c4a22f_0
-  - sqlite=3.45.3=h5eee18b_0
-  - tk=8.6.14=h39e8969_0
-  - traits=6.3.2=py310h5764c6d_1
-  - typing_extensions=4.12.2=pyha770c72_0
-  - tzdata=2024a=h04d1e81_0
-  - unicodedata2=15.1.0=py310h2372a71_0
-  - wheel=0.43.0=py310h06a4308_0
-  - whoosh=2.7.4=py310hff52083_8
-  - xorg-libxau=1.0.11=hd590300_0
-  - xorg-libxdmcp=1.1.3=h7f98852_0
-  - xvfbwrapper=0.2.9=pyhd8ed1ab_1005
-  - xz=5.4.6=h5eee18b_1
-  - zlib=1.2.13=h5eee18b_1
-  - zstandard=0.22.0=py310h1275a96_0
-  - zstd=1.5.5=hc292b87_2
-  - pip:
-      - certifi==2021.10.8
-      - charset-normalizer==2.0.8
-      - dicom2nifti==2.3.0
-      - dicomanonymizer==0.0.1
-      - idna==3.3
-      - importlib-metadata==4.8.2
-      - multivolumefile==0.2.3
-      - nibabel==5.2.1
-      - pandas==1.4.2
-      - pillow==9.0.0
-      - py7zr==0.17.0
-      - pybcj==0.5.0
-      - pycryptodomex==3.12.0
-      - pydicom==2.2.2
-      - pyppmd==0.17.3
-      - python-dateutil==2.8.2
-      - python-dotenv==0.19.2
-      - pytz==2021.3
-      - pyzstd==0.15.0
-      - requests==2.26.0
-      - scipy==1.11.4
-      - simpleitk==2.1.1.2
-      - texttable==1.6.4
-      - tqdm==4.62.3
-      - typing-extensions==4.0.1
-      - urllib3==1.26.7
-      - zipp==3.6.0
-prefix: /home/alpron/softs/miniconda3/envs/test

From d705257d8ea1cf7292250da97f91e4b842e071c2 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Thu, 18 Jul 2024 16:37:50 +0200
Subject: [PATCH 15/18] [BF]: fix pip and conda installation syntax

---
 .github/workflows/conda-installation.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml
index 198d557..28bb172 100644
--- a/.github/workflows/conda-installation.yml
+++ b/.github/workflows/conda-installation.yml
@@ -18,9 +18,11 @@ jobs:
           auto-update-conda: true
           activate-environment: working-env
           python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
       - name: Install dependencies
+        shell:  bash -el {0}
         run: |
-          python -m pip install -e .
+          python -m pip install .
           conda install -c conda-forge heudiconv git-annex=*alldep datalaad
 
       # Create virtual env under each python version

From 376fb2015e9d5c6c67bd79423814b46f28023943 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Thu, 18 Jul 2024 16:41:13 +0200
Subject: [PATCH 16/18] [BF]: fix conda syntax for build

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

diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml
index 28bb172..c87cba9 100644
--- a/.github/workflows/conda-installation.yml
+++ b/.github/workflows/conda-installation.yml
@@ -23,7 +23,7 @@ jobs:
         shell:  bash -el {0}
         run: |
           python -m pip install .
-          conda install -c conda-forge heudiconv git-annex=*alldep datalaad
+          conda install -c conda-forge heudiconv git-annex=*=alldep* datalad
 
       # Create virtual env under each python version
       # (optional and a bit redundant because we are already on a specific python)

From 957746ae109fe774df2f3a4b3874a62e304a53cf Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Thu, 18 Jul 2024 16:50:38 +0200
Subject: [PATCH 17/18] [BF]: updated installation instructions

---
 README.md | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index e0c44ab..28fb461 100644
--- a/README.md
+++ b/README.md
@@ -18,9 +18,13 @@ Optionally, rename the `.env.example` to `.env` and set the variables (`shanoir_
 
 ### Installation with conda
 > [!IMPORTANT]
-> This installation is required if shanoir2bids.py is used 
+> This installation method is required if shanoir2bids.py is used 
 
-After installing a (mini)conda distribution type in a terminal  `conda create -f environment.yml` then activate the environment using `conda activate working-env` where `working-env` is the default name of the created environment 
+In an active conda virtual environment type 
+```
+pip install . 
+conda install -c conda-forge heudiconv git-annex=*=alldep* datalad
+```
 ## Usage
 
 There are three scripts to download datasets:

From cbbe985aed8a75b3f826062100a0b75b853e4378 Mon Sep 17 00:00:00 2001
From: Alexandre Pron <alexandre.pron@gmail.com>
Date: Fri, 19 Jul 2024 14:26:43 +0200
Subject: [PATCH 18/18] [BF]: updated conda installation and instructions so
 that pip packages are conda dependencies

---
 .github/workflows/conda-installation.yml | 4 +++-
 README.md                                | 7 ++++++-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/conda-installation.yml b/.github/workflows/conda-installation.yml
index c87cba9..c7d1079 100644
--- a/.github/workflows/conda-installation.yml
+++ b/.github/workflows/conda-installation.yml
@@ -22,8 +22,10 @@ jobs:
       - name: Install dependencies
         shell:  bash -el {0}
         run: |
+          conda config --set pip_interop_enabled True
           python -m pip install .
-          conda install -c conda-forge heudiconv git-annex=*=alldep* datalad
+          conda update --all
+          conda install -c conda-forge heudiconv bids-validator dcm2niix git-annex=*=alldep* datalad 
 
       # Create virtual env under each python version
       # (optional and a bit redundant because we are already on a specific python)
diff --git a/README.md b/README.md
index 28fb461..eaeb567 100644
--- a/README.md
+++ b/README.md
@@ -21,8 +21,13 @@ Optionally, rename the `.env.example` to `.env` and set the variables (`shanoir_
 > This installation method is required if shanoir2bids.py is used 
 
 In an active conda virtual environment type 
-```
+```bash
+#use pip packages as dependencies
+conda config --set pip_interop_enabled True
 pip install . 
+#replace pip packages with conda packages when equivalent
+conda update --all
+# install missing conda packages (far simpler than using pip)
 conda install -c conda-forge heudiconv git-annex=*=alldep* datalad
 ```
 ## Usage