Release 0.8.0

.github/workflows/run-pytest.yml

@@ -11,14 +11,14 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.6, 3.9]
+        python-version: ["3.10", "3.14"]
         os: [ubuntu-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

.gitignore

@@ -81,4 +81,6 @@ bulker.egg-info/
 
 docs_jupyter/biobase_example
 docs_jupyter/templates/
-docs_jupyter/fasterq*
+docs_jupyter/fasterq*
+
+build

build/lib/bulker/_version.py

@@ -0,0 +1 @@
+__version__ = "0.7.3"

bulker/_version.py

@@ -1 +1 @@
-__version__ = "0.7.3"
+__version__ = "0.8.0"

bulker/templates/bulker_config.yaml

@@ -1,16 +1,18 @@
 bulker:
-  volumes: ['$HOME']
-  envvars: ['DISPLAY']
+  build_template: templates/docker_build.jinja2
+  container_engine: docker
+  crates: null
+  default_crate_folder: ${HOME}/bulker_crates
+  default_namespace: bulker
+  envvars:
+  - DISPLAY
+  executable_template: templates/docker_executable.jinja2
+  rcfile: templates/start.sh
+  rcfile_strict: templates/start_strict.sh
   registry_url: http://hub.bulker.io/
   shell_path: ${SHELL}
   shell_rc: $HOME/.bashrc
-  rcfile: start.sh
-  rcfile_strict: start_strict.sh  
-  default_crate_folder: ${HOME}/bulker_crates
+  shell_template: templates/docker_shell.jinja2
   singularity_image_folder: ${HOME}/simages
-  container_engine: docker
-  default_namespace: bulker
-  executable_template: docker_executable.jinja2
-  shell_template: docker_shell.jinja2
-  build_template: docker_build.jinja2
-  crates: null
+  volumes:
+  - $HOME

docs/changelog.md

@@ -1,12 +1,19 @@
 # Changelog
 
+## [0.8.0] -- 2026-02-25
+- Migrated to yacman v1 API (`YAMLConfigManager.from_yaml_file()`, `write_lock` context managers)
+- Dropped attmap dependency
+- Bumped ubiquerg requirement to >=0.9.0
+- Added support for Python 3.12
+- Fixed compatibility with distutils removal in Python 3.12
+
 ## [0.7.3] -- 2021-12-08
 - Fixed a bug that prevented use when installed in non-writable directory
 - Added ability to use bash autocompletion
 
 ## [0.7.2] -- 2021-06-24
 - Update to yacman 0.8.0, fixing references to internal config attributes.
-- Add documentation and clarity for the `shell_prompt` option
+- Added documentation and clarity for the `shell_prompt` option
 - Fixed bug with relative crate root folders
 
 ## [0.7.1] -- 2021-03-03

docs/settings.md

@@ -16,7 +16,7 @@ bulker:
         default:
           docker_args: -v /project/shefflab/database/redis:/data
     bioconductor:
-      bioconductor_full:
+      bioconductor_docker:
         default:
           docker_args: --volume=${HOME}/.local/lib/R:/usr/local/lib/R/host-site-library
         devel:
@@ -25,4 +25,4 @@ bulker:
 
 For the `redis` example, we're mounting a custom folder to `/data`, but only on `docker:redis` containers. 
 
-For the bioconductor example, we're showing how you can mount different host folders to the same container spot, depending on the *tag* (version) of the image being used. This is useful for separating your development vs. stable R packages, for example.
+For the bioconductor example, we're showing how you can mount different host folders to the same container spot, depending on the *tag* (version) of the image being used. This is useful for separating your development vs. stable R packages, for example.

requirements/requirements-all.txt

@@ -1,6 +1,6 @@
-yacman>=0.8.4
+yacman>=0.9.5
 pyyaml>=5.1
 logmuse>=0.2.0
 jinja2
-ubiquerg>=0.5.1
+ubiquerg>=0.9.0
 psutil

setup.py

@@ -32,11 +32,13 @@
     description="Manager of portable multi-container computing environments",
     long_description=long_description,
     long_description_content_type='text/markdown',
+    python_requires=">=3.10",
     classifiers=[
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Topic :: Scientific/Engineering :: Bio-Informatics"
     ],
     keywords="docker, containers, reproducibility, bioinformatics, workflow",

tests/test_bulker.py

@@ -16,9 +16,9 @@
 
 def test_yacman():
 
-    bc = yacman.YacAttMap(filepath=DEFAULT_CONFIG_FILEPATH)
+    bc = yacman.YAMLConfigManager.from_yaml_file(DEFAULT_CONFIG_FILEPATH)
     bc
-    bc.bulker.default_crate_folder
+    bc["bulker"]["default_crate_folder"]
 
 yaml_str = """\
 ---
@@ -28,7 +28,7 @@ def test_yacman():
 
 def test_float_idx():
 
-    data = yacman.YacAttMap(yamldata=yaml_str)
+    data = yacman.YAMLConfigManager.from_yaml_data(yaml_str)
     # We should be able to access this by string, not by int index.
     assert(data['2'] == "two")
     with pytest.raises(KeyError):
@@ -51,7 +51,7 @@ def test_bulker_init():
         pass
 
     bulker_init(DUMMY_CFG_FILEPATH, DEFAULT_CONFIG_FILEPATH, "docker")
-    bulker_config = yacman.YacAttMap(filepath=DEFAULT_CONFIG_FILEPATH)
+    bulker_config = yacman.YAMLConfigManager.from_yaml_file(DEFAULT_CONFIG_FILEPATH)
 
     manifest, cratevars = load_remote_registry_path(bulker_config, 
                                                      "demo",
@@ -66,7 +66,7 @@ def test_bulker_init():
 
 def test_bulker_activate():
 
-    bulker_config = yacman.YacAttMap(filepath=DEFAULT_CONFIG_FILEPATH)
+    bulker_config = yacman.YAMLConfigManager.from_yaml_file(DEFAULT_CONFIG_FILEPATH)
 
 
 def test_nonconfig_load():
@@ -85,23 +85,22 @@ def test_nonconfig_load():
         pass
 
     bulker_init(DUMMY_CFG_FILEPATH, DEFAULT_CONFIG_FILEPATH, "docker")
-    bulker_config = yacman.YacAttMap(filepath=DUMMY_CFG_FILEPATH)
+    bulker_config = yacman.YAMLConfigManager.from_yaml_file(DUMMY_CFG_FILEPATH)
 
     # The 'load' command will write the new crate to the config file;
     # we don't want it to update the template config file, so make a dummy
     # filepath that we'll delete later.
-    bulker_config.make_writable()
     # for testing, use a local crate folder
-    bulker_config.bulker.default_crate_folder = DUMMY_CFG_CRATE_SUBDIR
+    bulker_config["bulker"]["default_crate_folder"] = DUMMY_CFG_CRATE_SUBDIR
 
     print("Bulker config: {}".format(bulker_config))
     manifest, cratevars = load_remote_registry_path(bulker_config, 
                                                      "demo",
                                                      None)
     manifest, cratevars = load_remote_registry_path(bulker_config, "demo", None)
-    exe_template = mkabs(bulker_config.bulker.executable_template, os.path.dirname(bulker_config.__internal.file_path))
-    shell_template = mkabs(bulker_config.bulker.shell_template,
-                         os.path.dirname(bulker_config.__internal.file_path))        
+    exe_template = mkabs(bulker_config["bulker"]["executable_template"], os.path.dirname(bulker_config.filepath))
+    shell_template = mkabs(bulker_config["bulker"]["shell_template"],
+                         os.path.dirname(bulker_config.filepath))        
     import jinja2
     with open(exe_template, 'r') as f:
         contents = f.read()
@@ -111,8 +110,6 @@ def test_nonconfig_load():
         contents = f.read()
         shell_template_jinja = jinja2.Template(contents)
 
-
-
     bulker_load(manifest, cratevars, bulker_config, exe_template_jinja,
     shell_template_jinja, force=True)
     # bulker_config.make_readonly()  # deprecated this line with yacman improvements?
@@ -124,7 +121,7 @@ def test_nonconfig_load():
     print(cratelist)
 
     # Test a reload with already-removed crate
-    crate_folder = os.path.join(bulker_config.bulker.default_crate_folder, "bulker/demo/default")
+    crate_folder = os.path.join(bulker_config["bulker"]["default_crate_folder"], "bulker/demo/default")
     print("removing {}".format(crate_folder))
     # shutil.rmtree(crate_folder)
     bulker_load(manifest, cratevars, bulker_config, exe_template_jinja,
@@ -163,5 +160,5 @@ def test_nonconfig_load():
 # out, err, exitcode = capture([os.path.expandvars("$HOME/.local/bin/bulker"), "load", "bogusbogus"])
 # assert exitcode == 1
 
-# manifest = yacman.YacAttMap(filepath="/home/ns5bc/code/bulker/demo/demo_manifest.yaml")
+# manifest = yacman.YAMLConfigManager(filepath="/home/ns5bc/code/bulker/demo/demo_manifest.yaml")
 # bc