Use upstream ruamel.yaml instead of ruamel_yaml

docs/CMakeLists.txt

@@ -8,11 +8,10 @@ if (HAS_JSONSCHEMA EQUAL 1)
     message("python: missing `jsonschema` package is highly recommended")
 endif()
 
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import ruamel_yaml as yaml" RESULT_VARIABLE HAS_YAML1 ERROR_QUIET)
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import ruamel.yaml as yaml" RESULT_VARIABLE HAS_YAML2 ERROR_QUIET)
-execute_process(COMMAND ${Python_EXECUTABLE} -c "import yaml" RESULT_VARIABLE HAS_YAML3 ERROR_QUIET)
-if ((HAS_YAML1 EQUAL 1) AND (HAS_YAML2 EQUAL 1) AND (HAS_YAML3 EQUAL 1))
-    message("python: missing `ruamel_yaml` (preferred) or `yaml` packages are highly recommended")
+execute_process(COMMAND ${Python_EXECUTABLE} -c "import ruamel.yaml as yaml" RESULT_VARIABLE HAS_YAML1 ERROR_QUIET)
+execute_process(COMMAND ${Python_EXECUTABLE} -c "import yaml" RESULT_VARIABLE HAS_YAML2 ERROR_QUIET)
+if ((HAS_YAML1 EQUAL 1) AND (HAS_YAML2 EQUAL 1))
+    message("python: missing `ruamel.yaml` (preferred) or `yaml` packages are highly recommended")
 endif()
 
 find_program(PANDOC pandoc)

docs/_docs/install.md

@@ -59,7 +59,7 @@ but compile on most unix operating systems, including the Windows Subsystem for
 - CMake 3.24+
 - C++20 compiler (clang, g++, intel ixpc, ...)
 - Python 3.7+ with the following packages:
-  - `jinja2`, `ruamel_yaml` or `yaml`
+  - `jinja2`, `ruamel.yaml` or `yaml`
 
 The following are optional:
 

examples/temper/temper.ipynb

@@ -25,13 +25,12 @@
     "from math import log, fabs, pi, cos, sin\n",
     "from scipy.stats import ks_2samp\n",
     "try:\n",
-    "    try:\n",
-    "        import ruamel.yaml as yaml\n",
-    "    except ImportError:\n",
-    "        # anaconda packs it as a standalone module (underscore instead of dot)\n",
-    "        import ruamel_yaml as yaml\n",
+    "    import ruamel.yaml\n",
     "except ImportError:\n",
-    "    import yaml"
+    "    from yaml import safe_load as yaml_safe_load\n",
+    "else:\n",
+    "    def yaml_safe_load(stream):\n",
+    "        return ruamel.yaml.YAML(typ=\"safe\").load(stream)\n"
    ]
   },
   {
@@ -49,7 +48,7 @@
     "    template = jinja2.Template(template_file.read())\n",
     "    for replica, scale in enumerate(scale_array):\n",
     "        contents = template.render(scale=scale, micro=20000)\n",
-    "        yml = yaml.safe_load(contents) # parse contents as YAML\n",
+    "        yml = yaml_safe_load(contents) # parse contents as YAML\n",
     "        if not temper: \n",
     "            del yml[\"moves\"][1]\n",
     "        file = open(\"mpi{}.input.json\".format(replica), 'w')\n",

scripts/environment.yml

@@ -15,7 +15,7 @@ dependencies:
     - pandoc=2
     - pypandoc=1
     - beautifulsoup4=4.7
-    - ruamel_yaml=0.15
+    - ruamel.yaml=0.15
     - scipy=1.2
     - pygments=2.4
     - jinja2=2.10
@@ -25,5 +25,5 @@ dependencies:
     - jupyter_contrib_nbextensions=0.5
     - sdl2=2
     - jsonschema=3
-    - ruamel_yaml
+    - ruamel.yaml
 

scripts/extractsids.py

@@ -10,7 +10,13 @@
     sys.exit(1)
 
 import os, json, urllib.request
-import ruamel_yaml as yaml
+try:
+    import ruamel.yaml
+except ImportError:
+    from yaml import safe_load as yaml_safe_load
+else:
+    def yaml_safe_load(stream):
+        return ruamel.yaml.YAML(typ="safe").load(stream)
 
 if len(sys.argv)!=2:
     print("usage: {} music.yml".format(sys.argv[0]))
@@ -19,7 +25,7 @@
 filename = sys.argv[1]
 
 with open(filename) as f:
-    sidlist = yaml.safe_load(f)
+    sidlist = yaml_safe_load(f)
     server = sidlist['server'] + '/'
     dstdir = 'sids/'
     if not os.path.exists(dstdir):

scripts/inject_schema.py

@@ -18,12 +18,12 @@
 
 from jinja2 import Template
 try:
-    try:
-        import ruamel.yaml as yaml
-    except ImportError:
-        import ruamel_yaml as yaml
+    import ruamel.yaml
 except ImportError:
-    import yaml
+    from yaml import safe_load as yaml_safe_load
+else:
+    def yaml_safe_load(stream):
+        return ruamel.yaml.YAML(typ="safe").load(stream)
 
 def extract_as_lists(schema):
     '''
@@ -59,7 +59,7 @@ def print_table(schema, label='Keyword'):
 
 template = Template(sys.stdin.read()) # load template from stdin
 with open('schema.yml') as schema_file:
-    d = yaml.safe_load(schema_file)["properties"] # read schema file
+    d = yaml_safe_load(schema_file)["properties"] # read schema file
     atomlist = d["atomlist"]["items"]["additionalProperties"]
     out = template.render(topology_atomlist = print_table(atomlist, '`atomlist`'))
     print(out)

scripts/meta.yaml

@@ -24,7 +24,7 @@ requirements:
     - pandoc 2.*
     - pypandoc 1.*
     - beautifulsoup4
-    - ruamel_yaml
+    - ruamel.yaml
     - cmake >=3.11.4
     - numpy 1.*
     - matplotlib
@@ -37,7 +37,7 @@ requirements:
     - llvm-openmp    # [osx]
     - openmpi 1.6.*  # [osx]
     - openmpi 3.1.*  # [linux64]
-    - ruamel_yaml
+    - ruamel.yaml
     - pygments
     - numpy 1.*
     - python

scripts/yason.py

@@ -26,13 +26,19 @@
 # API compatibility between pyyaml and ruamel.yaml might break in the future
 # https://yaml.readthedocs.io/en/latest/api.html
 try:
-    try:
-        import ruamel.yaml as yaml
-    except ImportError:
-        # anaconda packs it as a standalone module (underscore instead of dot)
-        import ruamel_yaml as yaml
+    import ruamel.yaml as yaml
 except ImportError:
     import yaml
+    from yaml import (
+        safe_load as yaml_safe_load,
+        safe_dump as yaml_safe_dump,
+    )
+else:
+    def yaml_safe_load(stream):
+        return yaml.YAML(typ="safe").load(stream)
+
+    def yaml_safe_dump(data, stream=None, **kwargs):
+        return yaml.YAML(typ="safe").dump(data, stream=stream, **kwargs)
 
 try:
     pygments = True
@@ -108,7 +114,7 @@ def validate_input(instance):
             schemafile = os.path.abspath(pathname+subdir) + '/schema.yml'
             if os.path.exists(schemafile):
                 with open(schemafile, "r") as f:
-                    _schema = yaml.safe_load(f)
+                    _schema = yaml_safe_load(f)
                     error = best_match(Draft201909Validator(_schema).iter_errors(instance))
                     if error!=None:
                         eprint( "{}{}\n".format(human_readable_path(error.path), error.message) )
@@ -134,13 +140,13 @@ def validate_input(instance):
             i = highlight(out, JsonLexer(), formatter())
         print(i)
     else:
-        out = yaml.safe_dump(d, indent=args.indent, allow_unicode=True)
+        out = yaml_safe_dump(d, indent=args.indent, allow_unicode=True)
         if pygments:
             out = highlight(out, YamlLexer(), formatter())
         print(out)
 except json.decoder.JSONDecodeError:
     try:  # ... to read yaml
-        d = yaml.safe_load(i)  # plain load was deprecated in PyYAML
+        d = yaml_safe_load(i)  # plain load was deprecated in PyYAML
         if "mcloop" in d or "version" in d: 
             validate_input(d)
         out = json.dumps(d, indent=args.indent)

src/CMakeLists.txt

@@ -144,7 +144,7 @@ if (ENABLE_PYTHON)
     execute_process(COMMAND ${Python_EXECUTABLE} scripts/yason.py -h
         WORKING_DIRECTORY ${CMAKE_SOURCE_DIR} ERROR_QUIET OUTPUT_QUIET RESULT_VARIABLE yasontest)
     if (${yasontest} EQUAL 1)
-        message("missing required python modules 'yaml' or 'ruamel_yaml'")
+        message("missing required python modules 'yaml' or 'ruamel.yaml'")
     endif()
 
     pybind11_add_module(pyfaunus pyfaunus.cpp ${objs})