Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

fix(conda): add support pip deps for environment.yml files #6675

Merged
merged 3 commits into from
May 13, 2024
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
58 changes: 48 additions & 10 deletions pkg/dependency/parser/conda/environment/parse.go
Original file line number Diff line number Diff line change
@@ -15,7 +15,11 @@ import (
)

type environment struct {
Dependencies []Dependency `yaml:"dependencies"`
Entries []Entry `yaml:"dependencies"`
}

type Entry struct {
Dependencies []Dependency
}

type Dependency struct {
@@ -42,13 +46,15 @@ func (p *Parser) Parse(r xio.ReadSeekerAt) ([]ftypes.Package, []ftypes.Dependenc
}

var pkgs ftypes.Packages
for _, dep := range env.Dependencies {
pkg := p.toPackage(dep)
// Skip empty pkgs
if pkg.Name == "" {
continue
for _, entry := range env.Entries {
for _, dep := range entry.Dependencies {
pkg := p.toPackage(dep)
// Skip empty pkgs
if pkg.Name == "" {
continue
}
pkgs = append(pkgs, pkg)
}
pkgs = append(pkgs, pkg)
}

sort.Sort(pkgs)
@@ -96,8 +102,40 @@ func (*Parser) parseDependency(line string) (string, string) {
return name, parts[1]
}

func (d *Dependency) UnmarshalYAML(node *yaml.Node) error {
d.Value = node.Value
d.Line = node.Line
func (e *Entry) UnmarshalYAML(node *yaml.Node) error {
var dependencies []Dependency
// cf. https://github.com/go-yaml/yaml/blob/f6f7691b1fdeb513f56608cd2c32c51f8194bf51/resolve.go#L70-L81
switch node.Tag {
case "!!str":
dependencies = append(dependencies, Dependency{
Value: node.Value,
Line: node.Line,
})
case "!!map":
if node.Content != nil {
// Map key is package manager (e.g. pip). So we need to store only map values (dependencies).
// e.g. dependencies:
// - pip:
// - pandas==2.1.4
if node.Content[1].Tag != "!!seq" { // Conda supports only map[string][]string format.
return xerrors.Errorf("unsupported dependency type %q on line %d", node.Content[1].Tag, node.Content[1].Line)
}

for _, depContent := range node.Content[1].Content {
if depContent.Tag != "!!str" {
return xerrors.Errorf("unsupported dependency type %q on line %d", depContent.Tag, depContent.Line)
}

dependencies = append(dependencies, Dependency{
Value: depContent.Value,
Line: depContent.Line,
})
}
}
default:
return xerrors.Errorf("unsupported dependency type %q on line %d", node.Tag, node.Line)
}

e.Dependencies = dependencies
return nil
}
39 changes: 37 additions & 2 deletions pkg/dependency/parser/conda/environment/parse_test.go
Original file line number Diff line number Diff line change
@@ -31,6 +31,16 @@ func TestParse(t *testing.T) {
},
},
},
{
Name: "asgiref",
Version: "3.8.1",
Locations: ftypes.Locations{
{
StartLine: 21,
EndLine: 21,
},
},
},
{
Name: "blas",
Version: "1.0",
@@ -61,6 +71,16 @@ func TestParse(t *testing.T) {
},
},
},
{
Name: "django",
Version: "5.0.6",
Locations: ftypes.Locations{
{
StartLine: 22,
EndLine: 22,
},
},
},
{
Name: "ld_impl_linux-aarch64",
Locations: ftypes.Locations{
@@ -167,9 +187,24 @@ func TestParse(t *testing.T) {
},
},
{
name: "invalid_json",
name: "invalid yaml file",
input: "testdata/invalid.yaml",
wantErr: "unable to decode conda environment.yml file",
wantErr: "cannot unmarshal !!str `invalid` into environment.environment",
},
{
name: "`dependency` field uses unsupported type",
input: "testdata/wrong-deps-type.yaml",
wantErr: `unsupported dependency type "!!int" on line 5`,
},
{
name: "nested field uses unsupported type",
input: "testdata/wrong-nested-type.yaml",
wantErr: `unsupported dependency type "!!str" on line 5`,
},
{
name: "nested dependency uses unsupported type",
input: "testdata/wrong-nested-dep-type.yaml",
wantErr: `unsupported dependency type "!!map" on line 6`,
},
}
for _, tt := range tests {
3 changes: 3 additions & 0 deletions pkg/dependency/parser/conda/environment/testdata/happy.yaml
Original file line number Diff line number Diff line change
@@ -17,5 +17,8 @@ dependencies:
- liblapack=3.9.*=22_linuxaarch64_openblas
- libnsl=2.0.1=h31becfc_0
- bzip2=1.0.8=h998d150_5
- pip:
- asgiref==3.8.1
- django==5.0.6

prefix: /opt/conda/envs/test-env
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
name: test-env
channels:
- defaults
dependencies:
- 1

prefix: /opt/conda/envs/test-env
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
name: test-env
channels:
- defaults
dependencies:
- pip:
- wrongType:
- asgiref==3.8.1

prefix: /opt/conda/envs/test-env
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
name: test-env
channels:
- defaults
dependencies:
- pip: asgiref==3.8.1

prefix: /opt/conda/envs/test-env