Support multiple env yaml specs (#2993)

* tested and working

* docs update

* disallow multiple spec types

* add test for only one yaml specifies channel

* fix install yaml test

* Update micromamba/tests/test_create.py

Co-authored-by: Jonas Haag <jonas@lophus.org>

* Update micromamba/tests/test_create.py

Co-authored-by: Jonas Haag <jonas@lophus.org>

* suggestions

* separate loop

* appease the linter

* another test

---------

Co-authored-by: Jonas Haag <jonas@lophus.org>

dev/environment-micromamba-static.yml

@@ -1,6 +1,7 @@
 channels:
   - conda-forge
 dependencies:
+  - python >=3.12
   # libmamba build dependencies
   - cxx-compiler
   - cmake >=3.16

docs/source/installation/micromamba-installation.rst

@@ -188,7 +188,7 @@ To build from source, install the development dependencies, using a Conda compat
 
 .. code-block:: bash
 
-  micromamba create -n mamba --file dev/environment-static.yml
+  micromamba create -n mamba --file dev/environment-micromamba-static.yml
   micromamba activate -n mamba
 
 Use CMake from this environment to drive the build:

docs/source/user_guide/micromamba.rst

@@ -167,8 +167,8 @@ They are used the same way as text files:
 .. note::
   CLI options will keep :ref:`precedence<precedence-resolution>` over *target prefix* or *channels* specified in spec files.
 
-.. warning::
-  ``YAML`` spec files do not allow multiple files.
+.. note::
+  You can pass multiple ``YAML`` spec files by repeating the ``-f,--file`` argument.
 
 Explicit spec files
 *******************

libmamba/src/api/install.cpp

@@ -782,6 +782,14 @@ namespace mamba
 
     namespace detail
     {
+        enum SpecType
+        {
+            unknown,
+            env_lockfile,
+            yaml,
+            other
+        };
+
         void create_empty_target(const Context& context, const fs::u8path& prefix)
         {
             detail::create_target_directory(context, prefix);
@@ -816,12 +824,31 @@ namespace mamba
                 return;
             }
 
-            for (const auto& file : file_specs)
+            mamba::detail::SpecType spec_type = mamba::detail::unknown;
+            for (auto& file : file_specs)
             {
-                if (is_yaml_file_name(file) && file_specs.size() != 1)
+                mamba::detail::SpecType current_file_spec_type = mamba::detail::unknown;
+                if (is_env_lockfile_name(file))
                 {
-                    throw std::runtime_error("Can only handle 1 yaml file!");
+                    current_file_spec_type = mamba::detail::env_lockfile;
                 }
+                else if (is_yaml_file_name(file))
+                {
+                    current_file_spec_type = mamba::detail::yaml;
+                }
+                else
+                {
+                    current_file_spec_type = mamba::detail::other;
+                }
+
+                if (spec_type != mamba::detail::unknown && spec_type != current_file_spec_type)
+                {
+                    throw std::runtime_error(
+                        "found multiple spec file types, all spec files must be of same format (yaml, txt, explicit spec, etc.)"
+                    );
+                }
+
+                spec_type = current_file_spec_type;
             }
 
             for (auto& file : file_specs)
@@ -858,10 +885,15 @@ namespace mamba
                         channels.set_cli_value(updated_channels);
                     }
 
-                    if (parse_result.name.size() != 0)
+                    if (parse_result.name.size() != 0 && !env_name.configured())
                     {
                         env_name.set_cli_yaml_value(parse_result.name);
                     }
+                    else if (parse_result.name.size() != 0 && parse_result.name != env_name.value<std::string>())
+                    {
+                        LOG_WARNING << "YAML specs have different environment names. Using "
+                                    << env_name.value<std::string>();
+                    }
 
                     if (parse_result.dependencies.size() != 0)
                     {

micromamba/tests/test_create.py

@@ -318,15 +318,51 @@ def test_multiple_spec_files(tmp_home, tmp_root_prefix, tmp_path, type):
 
         cmd += ["-f", spec_file]
 
-    if type == "yaml":
-        with pytest.raises(subprocess.CalledProcessError):
-            helpers.create(*cmd, "--print-config-only")
-    else:
-        res = helpers.create(*cmd, "--print-config-only")
-        if type == "classic":
-            assert res["specs"] == specs
-        else:  # explicit
-            assert res["specs"] == [explicit_specs[0]]
+    res = helpers.create(*cmd, "--print-config-only")
+    if type == "yaml" or type == "classic":
+        assert res["specs"] == specs
+    else:  # explicit
+        assert res["specs"] == [explicit_specs[0]]
+
+
+@pytest.mark.parametrize("shared_pkgs_dirs", [True], indirect=True)
+def test_multiple_spec_files_different_types(tmp_home, tmp_root_prefix, tmp_path):
+    env_prefix = tmp_path / "myenv"
+
+    cmd = ["-p", env_prefix]
+
+    spec_file_1 = tmp_path / "env1.yaml"
+    spec_file_1.write_text("dependencies: [xtensor]")
+
+    spec_file_2 = tmp_path / "env2.txt"
+    spec_file_2.write_text("xsimd")
+
+    cmd += ["-f", spec_file_1, "-f", spec_file_2]
+
+    with pytest.raises(subprocess.CalledProcessError) as info:
+        helpers.create(*cmd, "--print-config-only")
+    assert "found multiple spec file types" in info.value.stderr.decode()
+
+
+@pytest.mark.parametrize("shared_pkgs_dirs", [True], indirect=True)
+def test_multiple_yaml_specs_only_one_has_channels(tmp_home, tmp_root_prefix, tmp_path):
+    env_prefix = tmp_path / "myenv"
+
+    cmd = ["-p", env_prefix]
+
+    spec_file_1 = tmp_path / "env1.yaml"
+    spec_file_1.write_text("dependencies: [xtensor]")
+
+    spec_file_2 = tmp_path / "env2.yaml"
+    spec_file_2.write_text(
+        "dependencies: [xsimd]\nchannels: [bioconda]",
+    )
+
+    cmd += ["-f", spec_file_1, "-f", spec_file_2]
+
+    res = helpers.create(*cmd, "--print-config-only", default_channel=False)
+    assert res["channels"] == ["bioconda"]
+    assert res["specs"] == ["xtensor", "xsimd"]
 
 
 def test_multiprocessing():

micromamba/tests/test_install.py

@@ -266,15 +266,11 @@ class TestInstall:
 
             cmd += ["-f", file]
 
-        if type == "yaml":
-            with pytest.raises(subprocess.CalledProcessError):
-                helpers.install(*cmd, "--print-config-only")
-        else:
-            res = helpers.install(*cmd, "--print-config-only")
-            if type == "classic":
-                assert res["specs"] == specs
-            else:  # explicit
-                assert res["specs"] == [explicit_specs[0]]
+        res = helpers.install(*cmd, "--print-config-only")
+        if type == "yaml" or type == "classic":
+            assert res["specs"] == specs
+        else:  # explicit
+            assert res["specs"] == [explicit_specs[0]]
 
     @pytest.mark.parametrize("priority", (None, "disabled", "flexible", "strict"))
     @pytest.mark.parametrize("no_priority", (None, True))

micromamba/tests/test_update.py

@@ -461,15 +461,11 @@ class TestUpdateConfig:
 
             cmd += ["-f", file]
 
-        if type == "yaml":
-            with pytest.raises(helpers.subprocess.CalledProcessError):
-                helpers.install(*cmd, "--print-config-only")
-        else:
-            res = helpers.install(*cmd, "--print-config-only")
-            if type == "classic":
-                assert res["specs"] == specs
-            else:  # explicit
-                assert res["specs"] == [explicit_specs[0]]
+        res = helpers.install(*cmd, "--print-config-only")
+        if type == "yaml" or type == "classic":
+            assert res["specs"] == specs
+        else:  # explicit
+            assert res["specs"] == [explicit_specs[0]]
 
     def test_channel_specific(self, env_created):
         helpers.install("quantstack::sphinx", no_dry_run=True)