[WiP] Draft for Gentoo configuration

neurodocker/cli/tests/test_build_images_with_cli.py

@@ -113,3 +113,23 @@ def test_json_roundtrip(cmd: str, inputs: str, tmp_path: Path):
         stdout, _ = run_fn(img, args=["env"])
         assert "CAT=FOO" in stdout
         assert "DOG=BAR" in stdout
+
+def test_gentoo_image(tmp_path: Path):
+    # also add singularity like in the test above
+
+    cmd = "docker"
+
+    _TemplateRegistry._reset()
+    runner = CliRunner()
+    result = runner.invoke(
+        generate,
+        [
+            cmd,
+            "--pkg-manager apt",
+            "--base-image neurodebian:bullseye",
+            "--ants version=2.4.3",
+            "--user nonroot"
+        ],
+    )
+    assert result.exit_code == 0, result.output
+    (tmp_path / "specs.json").write_text(result.output)

neurodocker/reproenv/types.py

@@ -18,8 +18,8 @@
 allowed_installation_methods = {"binaries", "source"}
 installation_methods_type = Literal["binaries", "source"]
 
-allowed_pkg_managers = {"apt", "yum"}
-pkg_managers_type = Literal["apt", "yum"]
+allowed_pkg_managers = {"apt", "portage", "yum"}
+pkg_managers_type = Literal["apt", "portage", "yum"]
 
 # Cross-reference the dictionary types below with the JSON schemas.
 

neurodocker/templates/afni.yaml

@@ -72,6 +72,8 @@ binaries:
         -   which
         -   unzip
         -   ncurses-compat-libs
+        portage:
+        -   sci-biology/ants
         debs:
         -   http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
         -   http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb

neurodocker/templates/gentoo.yaml

@@ -0,0 +1,49 @@
+---
+# Instructions to add NeuroDebian repositories.
+
+name: gentoo
+url: https://www.gentoo.org/
+binaries:
+    instructions: |
+        FROM docker.io/gentoo/portage:20240324 as portage
+        FROM docker.io/gentoo/stage3:20240318
+        # copy the entire portage volume in
+        COPY --from=portage /var/db/repos/gentoo /var/db/repos/gentoo
+        RUN emerge -v --noreplace dev-vcs/git
+        RUN emerge -v1u portage
+        # Pinned commits for the dependency tree state
+        ARG gentoo_hash=2d25617a1d085316761b06c17a93ec972f172fc6
+        ARG science_hash=73916dd3680ffd92e5bd3d32b262e5d78c86a448
+        ARG FEATURES="-ipc-sandbox -network-sandbox -pid-sandbox"
+        # This will be bound, and contents available outside of container
+        RUN mkdir /outputs
+        COPY .gentoo/portage/ /etc/portage/
+        # Moving gentoo repo from default rsync to git
+        RUN rm /var/db/repos/gentoo -rf
+        # Cloning manually to prevent vdb update, pinning state via git
+        # Allegedly it's better to chain everything in one command, something with container layers 🤔
+        RUN \
+                REPO_URL=$(grep "^sync-uri" /etc/portage/repos.conf/gentoo | sed -e "s/sync-uri *= *//g") && \
+                mkdir -p /var/db/repos/gentoo && pushd /var/db/repos/gentoo && git init . && \
+                        git remote add origin ${REPO_URL} && \
+                        git fetch --filter="blob:none" origin $gentoo_hash && \
+                        git reset --hard $gentoo_hash && rm .git -rf && popd && \
+                REPO_URL=$(grep "^sync-uri" /etc/portage/repos.conf/science | sed -e "s/sync-uri *= *//g") && \
+                mkdir -p /var/db/repos/science && pushd /var/db/repos/science && git init . && \
+                        git remote add origin ${REPO_URL} && \
+                        git fetch --filter="blob:none" origin $science_hash && \
+                        git reset --hard $science_hash && rm .git -rf && popd
+        # Old Christian: Remove sync-uri to not accidentally re-sync if we work with the package management interactively
+        # Christian from the future: Maybe we want the option to re-sync if we're debugging it interactively...
+        #RUN sed -i /etc/portage/repos.conf/{gentoo,science} -e "s/sync-type *= *git/sync-type =/g"
+        #RUN sed -i /etc/portage/repos.conf/{gentoo,science} -e "/sync-uri/d"
+        #RUN sed -i /etc/portage/repos.conf/{gentoo,science} -e "/sync-git-verify-commit-signature/d"
+        # Make sure all CPU flags supported by the hardware are whitelisted
+        # This only affects packages with handwritten assembly language optimizations, e.g. ffmpeg.
+        # Removing it is safe, software will just not take full advantage of processor capabilities.
+        #RUN emerge cpuid2cpuflags
+        #RUN echo "*/* $(cpuid2cpuflags)" > /etc/portage/package.use/00cpu-flags
+        ### Emerge cool stuff here
+        ### Autounmask-continue enables all features on dependencies which the top level packages require
+        ### By default this needs user confirmation which would interrupt the build.
+        RUN emerge --autounmask-continue afni fsl