Merge pull request #623 from mvdoc/fix/addheader

FIX add default header and entrypoint to docker and singularity files

neurodocker/cli/generate.py

@@ -307,6 +307,8 @@ def _get_params_for_registered_templates() -> list[click.Parameter]:
     names_tmpls = list(registered_templates_items())
     names_tmpls.sort(key=lambda r: r[0])  # sort by name
     for name, tmpl in names_tmpls:
+        if name.startswith("_"):  # Templates starting with _ are private
+            continue
         hlp = _create_help_for_template(Template(tmpl))
         param = OptionEatAll(
             [f"--{name.lower()}"], type=KeyValuePair(), multiple=True, help=hlp
@@ -438,6 +440,18 @@ def _base_generate(
     `generate singularity`. The difference between those two is the renderer used.
     """
     renderer_dict = _params_to_renderer_dict(ctx=ctx, pkg_manager=pkg_manager)
+
+    # Make sure to add default instructions if they are available among the templates
+    if "_default" in registered_templates():
+        # Add header to the instructions, after the base image.
+        renderer_dict["instructions"].insert(1, {"name": "_default", "kwds": {}})
+        # Use default entrypoint if user did not specify one.
+        instruction_names = [instr["name"] for instr in renderer_dict["instructions"]]
+        if "entrypoint" not in instruction_names:
+            renderer_dict["instructions"].append(
+                {"name": "entrypoint", "kwds": {"args": ["/neurodocker/startup.sh"]}}
+            )
+
     r = renderer.from_dict(renderer_dict)
 
     # Print the instructions in JSON if that's what the user wants.

neurodocker/cli/tests/test_cli.py

@@ -177,3 +177,43 @@ def test_render_registered(cmd: str, pkg_manager: str):
     assert result.exit_code == 0, result.output
     assert "jq-1.5/jq-linux64" in result.output
     assert "jq-1.6/jq-linux64" in result.output
+
+
+# Test that we add the default header and default/custom entrypoints
+@pytest.mark.parametrize("cmd", _cmds)
+@pytest.mark.parametrize("pkg_manager", ["apt", "yum"])
+@pytest.mark.parametrize("entrypoint", ["default", "custom"])
+def test_default_header_and_entrypoint(cmd: str, pkg_manager: str, entrypoint: str):
+    runner = CliRunner()
+    cmd_ = [
+        cmd,
+        "--base-image",
+        "debian:buster",
+        "--pkg-manager",
+        pkg_manager,
+    ]
+    if entrypoint == "custom":
+        cmd_.extend(["--entrypoint", "I", "decide"])
+    result = runner.invoke(generate, cmd_)
+    assert result.exit_code == 0, result.output
+
+    if cmd == "docker":
+        assert (
+            'ND_ENTRYPOINT="/neurodocker/startup.sh"\n'
+            'RUN export ND_ENTRYPOINT="/neurodocker/startup.sh"'
+        ) in result.output
+
+        if entrypoint == "default":
+            assert '\nENTRYPOINT ["/neurodocker/startup.sh"]\n' in result.output
+        else:
+            assert '\nENTRYPOINT ["I", "decide"]\n' in result.output
+    else:
+        assert (
+            '\nexport ND_ENTRYPOINT="/neurodocker/startup.sh"\n\n'
+            '%post\nexport ND_ENTRYPOINT="/neurodocker/startup.sh"\n'
+        ) in result.output
+
+        if entrypoint == "default":
+            assert "%runscript\n/neurodocker/startup.sh\n" in result.output
+        else:
+            assert "%runscript\nI decide\n" in result.output

neurodocker/templates/_header.yaml → neurodocker/templates/_default.yaml

@@ -4,7 +4,7 @@
 
 # TODO: read this about locales http://jaredmarkell.com/docker-and-locales/
 
-name: _header
+name: _default
 url: n/a
 # Not actually source, but we do not want to provide URLs.
 source:
@@ -28,14 +28,14 @@ source:
         LC_ALL: en_US.UTF-8
         ND_ENTRYPOINT: /neurodocker/startup.sh
     instructions: |
-        export ND_ENTRYPOINT="{{ _header._env['ND_ENTRYPOINT'] }}"
-        {{ _header.install_dependencies() }}
-        {%- if _header.pkg_manager == "apt" %}
-        sed -i -e 's/# {{ _header._env['LC_ALL'] }} UTF-8/{{ _header._env['LC_ALL'] }} UTF-8/' /etc/locale.gen
+        export ND_ENTRYPOINT="{{ self.env['ND_ENTRYPOINT'] }}"
+        {{ self.install_dependencies() }}
+        {%- if self.pkg_manager == "apt" %}
+        sed -i -e 's/# {{ self.env['LC_ALL'] }} UTF-8/{{ self.env['LC_ALL'] }} UTF-8/' /etc/locale.gen
         dpkg-reconfigure --frontend=noninteractive locales
-        update-locale LANG="{{ _header._env['LANG'] }}"
-        {%- elif _header.pkg_manager == "yum" %}
-        localedef -i {{ _header._env['LC_ALL'].split('.')[0] }} -f {{ _header._env['LC_ALL'].split('.')[1] }} {{ _header._env['LC_ALL'] }}
+        update-locale LANG="{{ self.env['LANG'] }}"
+        {%- elif self.pkg_manager == "yum" %}
+        localedef -i {{ self.env['LC_ALL'].split('.')[0] }} -f {{ self.env['LC_ALL'].split('.')[1] }} {{ self.env['LC_ALL'] }}
         {%- endif %}
         chmod 777 /opt && chmod a+s /opt
         mkdir -p /neurodocker