Provide base skeleton for gentoo to pass test_cli tests

neurodocker/cli/tests/test_cli.py

@@ -19,7 +19,7 @@ def test_fail_on_empty_args(cmd: str):
 
 
 @pytest.mark.parametrize("cmd", _cmds)
-@pytest.mark.parametrize("pkg_manager", ["apt", "yum"])
+@pytest.mark.parametrize("pkg_manager", ["apt", "portage", "yum"])
 def test_fail_on_no_base(cmd: str, pkg_manager: str):
     runner = CliRunner()
     result = runner.invoke(generate, [cmd, "--pkg-manager", pkg_manager])
@@ -34,7 +34,7 @@ def test_fail_on_no_pkg_manager(cmd: str):
 
 
 @pytest.mark.parametrize("cmd", _cmds)
-@pytest.mark.parametrize("pkg_manager", ["apt", "yum"])
+@pytest.mark.parametrize("pkg_manager", ["apt", "portage", "yum"])
 def test_minimal_args(cmd: str, pkg_manager: str):
     runner = CliRunner()
     result = runner.invoke(
@@ -107,7 +107,7 @@ def test_optioneatall_type_issue_498():
 
 
 @pytest.mark.parametrize("cmd", _cmds)
-@pytest.mark.parametrize("pkg_manager", ["apt", "yum"])
+@pytest.mark.parametrize("pkg_manager", ["apt", "portage", "yum"])
 def test_all_args(cmd: str, pkg_manager: str):
     runner = CliRunner()
     result = runner.invoke(
@@ -156,7 +156,7 @@ def test_all_args(cmd: str, pkg_manager: str):
 # is what registers the templates. Using the `docker` function
 # (`reproenv generate docker`) directly does not fire `generate`.
 @pytest.mark.parametrize("cmd", _cmds)
-@pytest.mark.parametrize("pkg_manager", ["apt", "yum"])
+@pytest.mark.parametrize("pkg_manager", ["apt", "portage", "yum"])
 def test_render_registered(cmd: str, pkg_manager: str):
     template_path = Path(__file__).parent
     runner = CliRunner(env={"REPROENV_TEMPLATE_PATH": str(template_path)})

neurodocker/reproenv/renderers.py

@@ -753,6 +753,8 @@ def _indent_run_instruction(string: str, indent=4) -> str:
 def _install(pkgs: list[str], pkg_manager: str, opts: str = None) -> str:
     if pkg_manager == "apt":
         return _apt_install(pkgs, opts)
+    elif pkg_manager == "portage":
+        return _portage_install(pkgs, opts)
     elif pkg_manager == "yum":
         return _yum_install(pkgs, opts)
     # TODO: add debs here?
@@ -802,6 +804,25 @@ def install_one(url: str):
     return s
 
 
+def _portage_install(pkgs: list[str], opts: str = None, sort=True) -> str:
+    """Return command to install packages with `portage` (Gentoo).
+
+    `opts` are options passed to `emerge`.
+    Default is "--autounmask-continue".
+    """
+    pkgs = sorted(pkgs) if sort else pkgs
+    opts = "--autounmask-continue" if opts is None else opts
+
+    s = """\
+emerge {opts} \\
+    {pkgs}
+rm -rf /var/tmp/portage/*
+""".format(
+        opts=opts, pkgs=" \\\n    ".join(pkgs)
+    )
+    return s.strip()
+
+
 def _yum_install(pkgs: list[str], opts: str = None, sort=True) -> str:
     """Return command to install packages with `yum` (CentOS, Fedora).
 

neurodocker/reproenv/schemas/renderer.json

@@ -11,10 +11,12 @@
       "type": "string",
       "enum": [
         "apt",
+        "portage",
         "yum"
       ],
       "examples": [
         "apt",
+        "portage",
         "yum"
       ]
     },

neurodocker/reproenv/types.py

@@ -32,6 +32,7 @@ class _InstallationDependenciesType(TypedDict, total=False):
 
     apt: list[str]
     debs: list[str]
+    portage: list[str]
     yum: list[str]
 
 

neurodocker/templates/gentoo-portage/make.conf

@@ -0,0 +1,21 @@
+### This file contains system-wide build variables, including Gentoo variables such as USE, which enable/disable optional package features.
+
+COMMON_FLAGS="-O2 -pipe -march=native"
+# Comment the following out on systems with less than 8 threads
+MAKEOPTS="--jobs 8 --load-average 9"
+CFLAGS="${COMMON_FLAGS}"
+CXXFLAGS="${COMMON_FLAGS}"
+FCFLAGS="${COMMON_FLAGS}"
+FFLAGS="${COMMON_FLAGS}"
+
+# NOTE: This stage was built with the bindist Use flag enabled
+
+# This sets the language of build output to English.
+# Please keep this setting intact when reporting bugs.
+LC_MESSAGES=C
+
+USE="${USE} science"
+ACCEPT_LICENSE="*"
+
+# Needed in the container environment
+#FEATURES="-ipc-sandbox -network-sandbox -pid-sandbox"

neurodocker/templates/gentoo-portage/package.accept_keywords/gen

@@ -0,0 +1,2 @@
+### This is needed because ::science packages are generally not marked as stable
+*/* ~amd64

neurodocker/templates/gentoo-portage/package.mask/bugs

@@ -0,0 +1,2 @@
+### This is empty, thankfully.
+### If we find bugs in some version of some package we can blacklist the package, version, or feature that causes it here.

neurodocker/templates/gentoo-portage/repos.conf/gentoo

@@ -0,0 +1,6 @@
+[gentoo]
+location = /var/db/repos/gentoo
+# We sync manually, but we need sync-uri to be written down somewhere to do so
+sync-type = git
+sync-uri = https://anongit.gentoo.org/git/repo/gentoo.git
+sync-git-verify-commit-signature = yes

neurodocker/templates/gentoo-portage/repos.conf/science

@@ -0,0 +1,6 @@
+[science]
+location = /var/db/repos/science
+# We sync manually, but we need sync-uri to be written down somewhere to do so
+sync-type = git
+sync-uri = https://anongit.gentoo.org/git/proj/sci.git
+priority = 7777

neurodocker/templates/gentoo.yaml

@@ -4,6 +4,11 @@
 name: gentoo
 url: https://www.gentoo.org/
 binaries:
+    # ATM template jsonschema demands having urls and instructions.
+    # In the future we might use urls to point to git repositories
+    # which are currently under gentoo-portage/ config files.
+    urls:
+        something: not-used
     instructions: |
         FROM docker.io/gentoo/portage:20240324 as portage
         FROM docker.io/gentoo/stage3:20240318
@@ -17,7 +22,7 @@ binaries:
         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/
+        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
@@ -46,4 +51,3 @@ binaries:
         ### 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