Merge pull request #57 from mrc-ide/rename-all

Rename project to pyorderly.

.github/workflows/test.yml

@@ -47,7 +47,7 @@ jobs:
       - name: Test install
         run: |
           pip install .
-          python -c "import orderly; import outpack"
+          python -c "import pyorderly"
       - name: Upload to Codecov
         uses: codecov/codecov-action@v4
         with:

README.md

@@ -1,7 +1,7 @@
-# outpack
+# pyorderly
 
-[![PyPI - Version](https://img.shields.io/pypi/v/outpack.svg)](https://pypi.org/project/outpack)
-[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/outpack.svg)](https://pypi.org/project/outpack)
+[![PyPI - Version](https://img.shields.io/pypi/v/pyorderly.svg)](https://pypi.org/project/pyorderly)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/pyorderly.svg)](https://pypi.org/project/pyorderly)
 
 -----
 
@@ -13,7 +13,7 @@
 ## Installation
 
 ```console
-pip install outpack
+pip install pyorderly
 ```
 
 ## Development
@@ -33,7 +33,7 @@ hatch run lint:fmt
 The outpack query parser is implemented in Rust as part of the
 [outpack_server](https://github.com/mrc-ide/outpack_server) repository. When
 developing new features in the query parser, they can be tested out in your
-development environment of `outpack-py` by installing the parser from your local
+development environment of `pyorderly` by installing the parser from your local
 checkout:
 
 ```
@@ -43,4 +43,4 @@ hatch run pip install /path/to/outpack_server
 
 ## License
 
-`outpack` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.
+`pyorderly` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.

docs/conf.py

@@ -5,7 +5,7 @@
 
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
-import outpack.__about__ as info
+import pyorderly.__about__ as info
 
 project = info.__name__
 copyright = "2023-present Imperial College of Science, Technology and Medicine"

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [project]
-name = "outpack"
+name = "pyorderly"
 dynamic = ["version"]
 description = "Reproducible and collaborative reporting"
 readme = "README.md"
@@ -36,15 +36,12 @@ dependencies = [
 ]
 
 [project.urls]
-Documentation = "https://github.com/mrc-ide/outpack#readme"
-Issues = "https://github.com/mrc-ide/outpack/issues"
-Source = "https://github.com/mrc-ide/outpack"
+Documentation = "https://github.com/mrc-ide/pyorderly#readme"
+Issues = "https://github.com/mrc-ide/pyorderly/issues"
+Source = "https://github.com/mrc-ide/pyorderly"
 
 [tool.hatch.version]
-path = "src/outpack/__about__.py"
-
-[tool.hatch.build.targets.wheel]
-packages = ["src/outpack", "src/orderly"]
+path = "src/pyorderly/__about__.py"
 
 [tool.hatch.envs.default]
 dependencies = [
@@ -177,14 +174,14 @@ ban-relative-imports = "all"
 convention = "numpy"
 
 [tool.coverage.run]
-source_pkgs = ["outpack", "orderly", "tests"]
+source_pkgs = ["pyorderly", "tests"]
 branch = true
 parallel = true
 
 # The wildcards are needed in order for the omit path to work correctly even
 # when spawning subprocess in different directories.
 omit = [
-  "**/src/outpack/__about__.py",
+  "**/src/pyorderly/__about__.py",
   "**/tests/helpers/*",
 ]
 

scripts/update_schemas

@@ -14,7 +14,7 @@ schema_version <-
   jsonlite::read_json(file.path(tmp, "schema", "config.json"))$version
 
 fs::dir_copy(file.path(tmp, "schema"), dest)
-writeLines(c("# Imported from outpack",
+writeLines(c("# Imported from pyorderly.outpack",
              "",
              sprintf("* Schema version %s", schema_version),
              sprintf("* Imported on %s", Sys.time()),

src/outpack/__about__.py → src/pyorderly/__about__.py

@@ -2,4 +2,4 @@
 #
 # SPDX-License-Identifier: MIT
 __version__ = "0.0.1"
-__name__ = "outpack-py"
+__name__ = "pyorderly"

src/orderly/__init__.py → src/pyorderly/__init__.py

@@ -1,4 +1,4 @@
-from orderly.core import (
+from pyorderly.core import (
     Parameters,
     artefact,
     dependency,

src/orderly/core.py → src/pyorderly/core.py

@@ -7,11 +7,11 @@
 
 from dataclasses_json import dataclass_json
 
-from orderly.current import get_active_context
-from outpack import util
-from outpack.copy_files import copy_files
-from outpack.search import search_unique
-from outpack.util import pl
+from pyorderly.current import get_active_context
+from pyorderly.outpack import util
+from pyorderly.outpack.copy_files import copy_files
+from pyorderly.outpack.search import search_unique
+from pyorderly.outpack.util import pl
 
 
 @dataclass_json()

src/orderly/current.py → src/pyorderly/current.py

@@ -3,9 +3,9 @@
 from pathlib import Path
 from typing import Optional
 
-from outpack.packet import Packet
-from outpack.root import OutpackRoot, root_open
-from outpack.search_options import SearchOptions
+from pyorderly.outpack.packet import Packet
+from pyorderly.outpack.root import OutpackRoot, root_open
+from pyorderly.outpack.search_options import SearchOptions
 
 
 class OrderlyCustomMetadata:

src/outpack/config.py → src/pyorderly/outpack/config.py

@@ -4,9 +4,9 @@
 
 from dataclasses_json import config, dataclass_json
 
-from outpack.schema import outpack_schema_version
-from outpack.static import LOCATION_TYPES
-from outpack.util import match_value
+from pyorderly.outpack.schema import outpack_schema_version
+from pyorderly.outpack.static import LOCATION_TYPES
+from pyorderly.outpack.util import match_value
 
 
 def read_config(root_path):

src/outpack/copy_files.py → src/pyorderly/outpack/copy_files.py

@@ -2,13 +2,13 @@
 from pathlib import Path
 from typing import Dict
 
-from outpack.location_pull import (
+from pyorderly.outpack.location_pull import (
     location_build_pull_plan,
     location_pull_files,
 )
-from outpack.metadata import PacketFile
-from outpack.root import OutpackRoot
-from outpack.search_options import SearchOptions
+from pyorderly.outpack.metadata import PacketFile
+from pyorderly.outpack.root import OutpackRoot
+from pyorderly.outpack.search_options import SearchOptions
 
 
 @dataclass

src/outpack/filestore.py → src/pyorderly/outpack/filestore.py

@@ -6,8 +6,8 @@
 from errno import ENOENT
 from pathlib import Path
 
-from outpack.hash import Hash, hash_parse, hash_validate_file
-from outpack.util import openable_temporary_file
+from pyorderly.outpack.hash import Hash, hash_parse, hash_validate_file
+from pyorderly.outpack.util import openable_temporary_file
 
 
 class FileStore:
@@ -79,8 +79,6 @@ def onerror(func, path, _exc_info):
             if not os.access(path, os.W_OK):
                 os.chmod(path, stat.S_IWUSR)
                 func(path)
-            else:
-                raise
 
         shutil.rmtree(self._path, onerror=onerror)
 

src/outpack/hash.py → src/pyorderly/outpack/hash.py

@@ -28,7 +28,7 @@ def hash_string(data, algorithm):
 
 
 def hash_parse(string):
-    if type(string) == Hash:
+    if isinstance(string, Hash):
         return string
     return Hash(*string.split(":"))
 

src/outpack/ids.py → src/pyorderly/outpack/ids.py

@@ -3,7 +3,7 @@
 import secrets
 import time
 
-from outpack.util import iso_time_str
+from pyorderly.outpack.util import iso_time_str
 
 RE_ID = re.compile("^[0-9]{8}-[0-9]{6}-[0-9a-f]{8}$")
 

src/outpack/index.py → src/pyorderly/outpack/index.py

@@ -2,7 +2,7 @@
 from dataclasses import dataclass
 from typing import Dict, List
 
-from outpack.metadata import (
+from pyorderly.outpack.metadata import (
     MetadataCore,
     PacketLocation,
     read_metadata_core,

src/outpack/init.py → src/pyorderly/outpack/init.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from outpack.config import Config, read_config, write_config
+from pyorderly.outpack.config import Config, read_config, write_config
 
 
 def outpack_init(

src/outpack/location.py → src/pyorderly/outpack/location.py

@@ -2,12 +2,12 @@
 import shutil
 from pathlib import PurePath
 
-from outpack.config import Location, update_config
-from outpack.location_driver import LocationDriver
-from outpack.location_path import OutpackLocationPath
-from outpack.location_ssh import OutpackLocationSSH, parse_ssh_url
-from outpack.root import OutpackRoot, root_open
-from outpack.static import (
+from pyorderly.outpack.config import Location, update_config
+from pyorderly.outpack.location_driver import LocationDriver
+from pyorderly.outpack.location_path import OutpackLocationPath
+from pyorderly.outpack.location_ssh import OutpackLocationSSH, parse_ssh_url
+from pyorderly.outpack.root import OutpackRoot, root_open
+from pyorderly.outpack.static import (
     LOCATION_LOCAL,
     LOCATION_ORPHAN,
     LOCATION_RESERVED_NAME,

src/outpack/location_driver.py → src/pyorderly/outpack/location_driver.py

@@ -2,7 +2,7 @@
 from contextlib import AbstractContextManager
 from typing import Dict, List
 
-from outpack.metadata import MetadataCore, PacketFile, PacketLocation
+from pyorderly.outpack.metadata import MetadataCore, PacketFile, PacketLocation
 
 
 class LocationDriver(AbstractContextManager):

src/outpack/location_path.py → src/pyorderly/outpack/location_path.py

@@ -2,11 +2,11 @@
 import shutil
 from typing import Dict, List
 
-from outpack.location_driver import LocationDriver
-from outpack.metadata import MetadataCore, PacketFile, PacketLocation
-from outpack.root import find_file_by_hash, root_open
-from outpack.static import LOCATION_LOCAL
-from outpack.util import read_string
+from pyorderly.outpack.location_driver import LocationDriver
+from pyorderly.outpack.metadata import MetadataCore, PacketFile, PacketLocation
+from pyorderly.outpack.root import find_file_by_hash, root_open
+from pyorderly.outpack.static import LOCATION_LOCAL
+from pyorderly.outpack.util import read_string
 
 
 class OutpackLocationPath(LocationDriver):

src/outpack/location_pull.py → src/pyorderly/outpack/location_pull.py

@@ -7,22 +7,27 @@
 
 import humanize
 
-from outpack.filestore import FileStore
-from outpack.hash import hash_validate_string
-from outpack.location import (
+from pyorderly.outpack.filestore import FileStore
+from pyorderly.outpack.hash import hash_validate_string
+from pyorderly.outpack.location import (
     LocationDriver,
     _location_driver,
     location_resolve_valid,
 )
-from outpack.metadata import (
+from pyorderly.outpack.metadata import (
     MetadataCore,
     PacketFileWithLocation,
     PacketLocation,
 )
-from outpack.root import OutpackRoot, find_file_by_hash, mark_known, root_open
-from outpack.search_options import SearchOptions
-from outpack.static import LOCATION_LOCAL
-from outpack.util import format_list, partition, pl
+from pyorderly.outpack.root import (
+    OutpackRoot,
+    find_file_by_hash,
+    mark_known,
+    root_open,
+)
+from pyorderly.outpack.search_options import SearchOptions
+from pyorderly.outpack.static import LOCATION_LOCAL
+from pyorderly.outpack.util import format_list, partition, pl
 
 
 def outpack_location_pull_metadata(location=None, root=None, *, locate=True):

src/outpack/location_ssh.py → src/pyorderly/outpack/location_ssh.py

@@ -7,12 +7,12 @@
 
 import paramiko
 
-from outpack.config import Config
-from outpack.hash import hash_parse
-from outpack.location_driver import LocationDriver
-from outpack.metadata import MetadataCore, PacketFile, PacketLocation
-from outpack.static import LOCATION_LOCAL
-from outpack.util import removeprefix
+from pyorderly.outpack.config import Config
+from pyorderly.outpack.hash import hash_parse
+from pyorderly.outpack.location_driver import LocationDriver
+from pyorderly.outpack.metadata import MetadataCore, PacketFile, PacketLocation
+from pyorderly.outpack.static import LOCATION_LOCAL
+from pyorderly.outpack.util import removeprefix
 
 
 def parse_ssh_url(url):

src/outpack/metadata.py → src/pyorderly/outpack/metadata.py

@@ -4,8 +4,8 @@
 
 from dataclasses_json import dataclass_json
 
-from outpack.hash import hash_file
-from outpack.tools import GitInfo
+from pyorderly.outpack.hash import hash_file
+from pyorderly.outpack.tools import GitInfo
 
 
 @dataclass_json()

src/outpack/packet.py → src/pyorderly/outpack/packet.py

@@ -2,20 +2,25 @@
 import time
 from pathlib import Path
 
-from outpack.copy_files import copy_files
-from outpack.hash import hash_file, hash_parse, hash_string, hash_validate_file
-from outpack.ids import outpack_id, validate_outpack_id
-from outpack.location_pull import outpack_location_pull_packet
-from outpack.metadata import (
+from pyorderly.outpack.copy_files import copy_files
+from pyorderly.outpack.hash import (
+    hash_file,
+    hash_parse,
+    hash_string,
+    hash_validate_file,
+)
+from pyorderly.outpack.ids import outpack_id, validate_outpack_id
+from pyorderly.outpack.location_pull import outpack_location_pull_packet
+from pyorderly.outpack.metadata import (
     MetadataCore,
     PacketDepends,
     PacketFile,
 )
-from outpack.root import mark_known, root_open
-from outpack.schema import outpack_schema_version, validate
-from outpack.search import as_query, search_unique
-from outpack.tools import git_info
-from outpack.util import all_normal_files, as_posix_path
+from pyorderly.outpack.root import mark_known, root_open
+from pyorderly.outpack.schema import outpack_schema_version, validate
+from pyorderly.outpack.search import as_query, search_unique
+from pyorderly.outpack.tools import git_info
+from pyorderly.outpack.util import all_normal_files, as_posix_path
 
 
 # TODO: most of these fields should be private.