ms-env 0.2.0__tar.gz

ms_env-0.2.0/.github/workflows/ci.yml

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+name: ci
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+          cache: pip
+      - run: pip install -e ".[dev]"
+      - run: pytest -q

ms_env-0.2.0/.github/workflows/docs.yml

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+name: Documentation
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  workflow_dispatch:
+
+concurrency:
+  group: documentation
+  cancel-in-progress: false
+
+# mike commits every version to the gh-pages branch and GitHub Pages serves that
+# branch (Settings > Pages > Deploy from a branch: gh-pages, / (root)).
+# An Actions Pages deployment is keyed by commit SHA, so a release tag on a
+# commit already deployed from main would be silently ignored.
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v6
+        with:
+          python-version: 3.x
+      - run: pip install zensical "mkdocstrings[python]" "mike @ git+https://github.com/squidfunk/mike.git"
+      - name: Configure Git author
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+      - name: Deploy development documentation
+        if: github.ref == 'refs/heads/main'
+        run: |
+          mike deploy --push dev
+          if ! mike list latest >/dev/null 2>&1; then
+            mike set-default --push dev
+          fi
+      - name: Deploy release documentation
+        if: startsWith(github.ref, 'refs/tags/v')
+        run: |
+          mike deploy --push --update-aliases --alias-type redirect "$GITHUB_REF_NAME" latest
+          mike set-default --push latest

ms_env-0.2.0/.github/workflows/publish.yml

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+# Publish to PyPI on a GitHub release.
+#
+# No secrets: the job authenticates to PyPI over OIDC (Trusted Publishing).
+# It has to be enabled on the PyPI side *before* the first upload -- for a
+# project that does not exist yet, that is a "pending publisher" under
+# Your projects > Publishing, and it must name this repo, `publish.yml`
+# and the `pypi` environment below.
+name: publish
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  pypi:
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      # A permissions block sets every scope it does not name to none, so
+      # checkout needs contents spelled out or it cannot read a private repo.
+      contents: read
+      id-token: write  # mint the OIDC token PyPI checks; no secret involved
+    steps:
+      - uses: actions/checkout@v7
+        with:
+          fetch-depth: 0  # setuptools-scm reads the version off the tag
+      - uses: actions/setup-python@v7
+        with:
+          python-version: "3.12"
+      - run: pipx run build
+      - uses: pypa/gh-action-pypi-publish@release/v1

ms_env-0.2.0/.gitignore

@@ -0,0 +1,220 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+*.lcov
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+# Pipfile.lock
+
+# uv
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi/*
+!.pixi/config.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule*
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs/Zensical documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#   and can be added to the global gitignore or merged into this file.  For a more nuclear
+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# Abstra
+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
+#   Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore that
+#   can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, you
+#   could uncomment the following to ignore the entire vscode folder
+# .vscode/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

ms_env-0.2.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 MolSuite
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

ms_env-0.2.0/PKG-INFO

@@ -0,0 +1,133 @@
+Metadata-Version: 2.4
+Name: ms_env
+Version: 0.2.0
+Summary: Environments for MolSuite apps: find or install external tools, on this machine or over ssh.
+Author: Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/MolSuite/ms_env
+Project-URL: Documentation, https://molsuite.github.io/ms_env/
+Project-URL: Issues, https://github.com/MolSuite/ms_env/issues
+Keywords: environments,conda,micromamba,ssh,molsuite
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Dynamic: license-file
+
+# ms_env
+
+Environments for MolSuite apps: find an external tool that already works, or install
+it, on this machine or on a host reached over `ssh`. Standard library only.
+
+A **recipe** says how to tell that a tool works and how to install it. A **host**
+says where. `ms_env` applies one to the other.
+
+```python
+from ms_env import READY, Host, ToolSpec, ensure, locate
+
+spec = ToolSpec.load("openbabel.toml")
+
+recipe = spec.recipe("/home/me/.myapp/tools")      # bound to this machine
+state, executable = locate(recipe)                  # (READY, ".../bin/obabel") or (MISSING, "")
+if state != READY:
+    install = ensure(recipe)                        # returns at once: a daemon thread installs
+    install.future.result()                         # wait; `install.lines` is the live log
+
+cluster = Host("me@login.hpc")                    # as `ssh` knows it
+ensure(spec.recipe("/home/me/.myapp/tools"), cluster).future.result()
+```
+
+## A recipe
+
+One TOML file per tool, shipped by the app:
+
+```toml
+[tool]
+name = "openbabel"
+label = "OpenBabel"
+version = "3.1.1"                         # pinned here; never a user option
+prefix = "{tools_home}/{name}/{version}"  # the default
+
+[locate]
+paths = ["{prefix}/bin/obabel"]           # where the install puts it
+commands = ["obabel"]                     # looked up on PATH
+check = ["{exe}", "-V"]                   # {exe} = the candidate
+
+[env]                                     # a conda prefix at {prefix}
+conda = ["openbabel={version}"]
+pip = []
+
+[[install]]                               # plain steps, after [env]
+name = "download the model"
+argv = ["curl", "-fsSL", "-o", "{prefix}/model.pt", "https://..."]
+timeout = 1800
+```
+
+Lookup on a host, first candidate whose check exits 0 wins: the paths the user
+registered, the managed install under `tools_home`, then `PATH`. `[env]` is created
+with micromamba: the one on the host's `PATH`, or one downloaded into `tools_home`.
+Another conda-type program is used only when the app names it (`manager=`).
+
+## Whose an environment is
+
+`ensure` stamps the prefix it installs. The stamp decides what may happen to it:
+
+| At the prefix | `ensure` | `remove` |
+|---|---|---|
+| Nothing | Creates it | Nothing to delete |
+| A stamp of this recipe | Nothing | Deletes it |
+| A stamp of another recipe (the TOML changed) | Creates it again: the update | Deletes it |
+| Something without a stamp: the user's own environment | Verifies it, never changes it | Leaves it |
+
+```python
+from ms_env import remove, verify
+
+mine = spec.recipe("/home/me/.myapp/tools", prefix="/home/me/envs/babel")   # an environment I already have
+verify(mine)    # [] when it meets the recipe, else what it lacks:
+                # ["conda: openbabel=3.1.1 is asked for and is not there"]
+remove(recipe)  # True: ms_env had installed it and it is gone
+```
+
+`verify` looks up every pinned conda package, every pinned pip package and the
+recipe's check, and only reads. An executable registered on its own (`extra_paths=`)
+is not an environment: it only has to pass the check.
+
+`ensure(recipe, host, busy=why)` asks `why()` before it changes an install of its own:
+a reason (`"2 jobs are running from it"`) makes the install fail and leaves the prefix
+as it is.
+
+## A host
+
+`Host()` is this machine. `Host("me@login.hpc")` runs every command through the system's
+`ssh` with `BatchMode=yes`: users, keys and jumps come from `~/.ssh/config`, the key
+logs in or the command fails at once, no credential is handled and nothing is left
+listening on the other side. A host is a POSIX machine; only Linux is supported.
+
+## The environment of an app
+
+`app_recipe` makes the recipe that gives a host the environment an app runs in here:
+the same Python, the same versions, and the code of a source checkout as it is now.
+
+```python
+from ms_env import app_recipe
+
+home = cluster.home()
+recipe = app_recipe("myapp", ["myapp"], ["myapp"], prefix=f"{home}/.myapp/env",
+                    tools_home=f"{home}/.myapp/tools", cache="/home/me/.myapp/cache/wheels")
+ensure(recipe, cluster).future.result()
+```
+
+## Install
+
+```bash
+pip install ms_env
+```
+
+Documentation: <https://molsuite.github.io/ms_env/>

ms_env-0.2.0/README.md

@@ -0,0 +1,110 @@
+# ms_env
+
+Environments for MolSuite apps: find an external tool that already works, or install
+it, on this machine or on a host reached over `ssh`. Standard library only.
+
+A **recipe** says how to tell that a tool works and how to install it. A **host**
+says where. `ms_env` applies one to the other.
+
+```python
+from ms_env import READY, Host, ToolSpec, ensure, locate
+
+spec = ToolSpec.load("openbabel.toml")
+
+recipe = spec.recipe("/home/me/.myapp/tools")      # bound to this machine
+state, executable = locate(recipe)                  # (READY, ".../bin/obabel") or (MISSING, "")
+if state != READY:
+    install = ensure(recipe)                        # returns at once: a daemon thread installs
+    install.future.result()                         # wait; `install.lines` is the live log
+
+cluster = Host("me@login.hpc")                    # as `ssh` knows it
+ensure(spec.recipe("/home/me/.myapp/tools"), cluster).future.result()
+```
+
+## A recipe
+
+One TOML file per tool, shipped by the app:
+
+```toml
+[tool]
+name = "openbabel"
+label = "OpenBabel"
+version = "3.1.1"                         # pinned here; never a user option
+prefix = "{tools_home}/{name}/{version}"  # the default
+
+[locate]
+paths = ["{prefix}/bin/obabel"]           # where the install puts it
+commands = ["obabel"]                     # looked up on PATH
+check = ["{exe}", "-V"]                   # {exe} = the candidate
+
+[env]                                     # a conda prefix at {prefix}
+conda = ["openbabel={version}"]
+pip = []
+
+[[install]]                               # plain steps, after [env]
+name = "download the model"
+argv = ["curl", "-fsSL", "-o", "{prefix}/model.pt", "https://..."]
+timeout = 1800
+```
+
+Lookup on a host, first candidate whose check exits 0 wins: the paths the user
+registered, the managed install under `tools_home`, then `PATH`. `[env]` is created
+with micromamba: the one on the host's `PATH`, or one downloaded into `tools_home`.
+Another conda-type program is used only when the app names it (`manager=`).
+
+## Whose an environment is
+
+`ensure` stamps the prefix it installs. The stamp decides what may happen to it:
+
+| At the prefix | `ensure` | `remove` |
+|---|---|---|
+| Nothing | Creates it | Nothing to delete |
+| A stamp of this recipe | Nothing | Deletes it |
+| A stamp of another recipe (the TOML changed) | Creates it again: the update | Deletes it |
+| Something without a stamp: the user's own environment | Verifies it, never changes it | Leaves it |
+
+```python
+from ms_env import remove, verify
+
+mine = spec.recipe("/home/me/.myapp/tools", prefix="/home/me/envs/babel")   # an environment I already have
+verify(mine)    # [] when it meets the recipe, else what it lacks:
+                # ["conda: openbabel=3.1.1 is asked for and is not there"]
+remove(recipe)  # True: ms_env had installed it and it is gone
+```
+
+`verify` looks up every pinned conda package, every pinned pip package and the
+recipe's check, and only reads. An executable registered on its own (`extra_paths=`)
+is not an environment: it only has to pass the check.
+
+`ensure(recipe, host, busy=why)` asks `why()` before it changes an install of its own:
+a reason (`"2 jobs are running from it"`) makes the install fail and leaves the prefix
+as it is.
+
+## A host
+
+`Host()` is this machine. `Host("me@login.hpc")` runs every command through the system's
+`ssh` with `BatchMode=yes`: users, keys and jumps come from `~/.ssh/config`, the key
+logs in or the command fails at once, no credential is handled and nothing is left
+listening on the other side. A host is a POSIX machine; only Linux is supported.
+
+## The environment of an app
+
+`app_recipe` makes the recipe that gives a host the environment an app runs in here:
+the same Python, the same versions, and the code of a source checkout as it is now.
+
+```python
+from ms_env import app_recipe
+
+home = cluster.home()
+recipe = app_recipe("myapp", ["myapp"], ["myapp"], prefix=f"{home}/.myapp/env",
+                    tools_home=f"{home}/.myapp/tools", cache="/home/me/.myapp/cache/wheels")
+ensure(recipe, cluster).future.result()
+```
+
+## Install
+
+```bash
+pip install ms_env
+```
+
+Documentation: <https://molsuite.github.io/ms_env/>

ms_env-0.2.0/docs/api_reference.md

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+# API reference
+
+Every name is imported from `ms_env`.
+
+::: ms_env