update build_examples without file-local yml lsp config

graeter-group · Oct 25, 2023 · 656ec36 · 656ec36
1 parent a4ea59e
commit 656ec36
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Showing 14 changed files with 2 additions and 42 deletions.
diff --git a/example/alanine_hat_naive/kimmdy.yml b/example/alanine_hat_naive/kimmdy.yml
@@ -1,11 +1,11 @@
-# yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json
 dryrun: false
 name: 'alanine_hat_000'
 max_tasks: 100
 gromacs_alias: 'gmx'
 gmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1
 ff: 'amber99sb-star-ildnp.ff' # optional, dir endinng with .ff by default 
 top: 'Ala_out.top'
+gro: 'npt.gro'
 ndx: 'index.ndx'
 mds:
   equilibrium:

diff --git a/example/charged_peptide_homolysis_hat_naive/kimmdy.yml b/example/charged_peptide_homolysis_hat_naive/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json
-
 name: 'kimmdy_001'
 dryrun: false
 max_tasks: 100

diff --git a/example/hexalanine_homolysis/kimmdy.yml b/example/hexalanine_homolysis/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json
-
 dryrun: false
 name: 'hexalanine_homolysis_000'
 max_tasks: 100

diff --git a/example/hexalanine_single_reaction/kimmdy.yml b/example/hexalanine_single_reaction/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json
-
 dryrun: false
 name: 'single_reaction_000'
 gmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1

diff --git a/example/triplehelix_pull/kimmdy.yml b/example/triplehelix_pull/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../src/kimmdy/kimmdy-yaml-schema.json
-
 name: 'kimmdy_001'
 dryrun: false
 max_tasks: 10

diff --git a/src/kimmdy/tools.py b/src/kimmdy/tools.py
@@ -50,23 +50,7 @@ def build_examples(restore: str):
                 assets_path / "amber99sb-star-ildnp.ff",
                 target_is_directory=True,
             )
-            kimmdy_yml_schema_path = dest / "kimmdy.yml"
-            if kimmdy_yml_schema_path.exists():
-                schema_path = (
-                    Path("..") / ".." / "src" / "kimmdy" / "kimmdy-yaml-schema.json"
-                )
-                first_line = f"# yaml-language-server: $schema={schema_path}\n"
-                with open(kimmdy_yml_schema_path, "r+") as f:
-                    lines = f.readlines()
-                    if lines[0][:22] == "# yaml-language-server":
-                        lines[0] = first_line
-                    else:
-                        lines = [first_line] + lines
-                    f.seek(0)
-                    f.writelines(lines)
-                    f.truncate()
-
-            print("done")
+            print("done building examples")
         except FileExistsError as e:
             raise FileExistsError(
                 f"Could not build example directory {directory} because it already exists. Try the --restore option to still build it."

diff --git a/tests/test_files/test_integration/alanine_hat_naive/kimmdy.yml b/tests/test_files/test_integration/alanine_hat_naive/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../../../src/kimmdy/kimmdy-yaml-schema.json
-
 dryrun: false
 name: 'alanine_hat_000'
 max_tasks: 100

diff --git a/tests/test_files/test_integration/charged_peptide_homolysis_hat_naive/kimmdy.yml b/tests/test_files/test_integration/charged_peptide_homolysis_hat_naive/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../../../src/kimmdy/kimmdy-yaml-schema.json
-
 name: 'kimmdy_001'
 dryrun: false
 max_tasks: 100

diff --git a/tests/test_files/test_integration/emptyrun/kimmdy.yml b/tests/test_files/test_integration/emptyrun/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../../../src/kimmdy/kimmdy-yaml-schema.json
-
 name: 'emptyrun_001'
 dryrun: false
 max_tasks: 0

diff --git a/tests/test_files/test_integration/hexalanine_homolysis/kimmdy.yml b/tests/test_files/test_integration/hexalanine_homolysis/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../../../src/kimmdy/kimmdy-yaml-schema.json
-
 dryrun: false
 name: 'hexalanine_homolysis_000'
 max_tasks: 100

diff --git a/tests/test_files/test_integration/hexalanine_single_reaction/kimmdy.yml b/tests/test_files/test_integration/hexalanine_single_reaction/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../../../src/kimmdy/kimmdy-yaml-schema.json
-
 dryrun: false
 name: 'single_reaction_000'
 gmx_mdrun_flags: -maxh 24 -dlb yes -nt 8 -npme 0 -ntmpi 1

diff --git a/tests/test_files/test_integration/minimal_input_files/kimmdy.yml b/tests/test_files/test_integration/minimal_input_files/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../../../src/kimmdy/kimmdy-yaml-schema.json
-
 name: 'minimal'
 dryrun: true
 max_tasks: 0

diff --git a/tests/test_files/test_integration/triplehelix_pull/kimmdy.yml b/tests/test_files/test_integration/triplehelix_pull/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../../../src/kimmdy/kimmdy-yaml-schema.json
-
 name: 'kimmdy_001'
 dryrun: false
 max_tasks: 10

diff --git a/tests/test_files/test_schema/kimmdy.yml b/tests/test_files/test_schema/kimmdy.yml
@@ -1,5 +1,3 @@
-# yaml-language-server: $schema=../../../src/kimmdy/kimmdy-yaml-schema.json
-
 name: 'kimmdy_001'
 dryrun: false
 max_tasks: 100