cellpy 2.0.0a1__tar.gz → 2.0.0a2__tar.gz

cellpy-2.0.0a2/.issueflows/03-solved-issues/issue375_original.md

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+# Issue #375: Add support for remote paths for raw data and cellpy data access
+
+Source: https://github.com/jepegit/cellpy/issues/375
+
+## Original issue text
+
+- Loading raw data from remote locations
+- Searching/listing remote raw-data directories
+- Reading and possibly writing cellpy files stored remotely
+- handling of authentication and credentials
+- when direct remote access is not possible: Predictable local caching / temporary copy behavior 
+
+ ## Questions to resolve
+  - Which remote schemes do we want to support initially?
+      - ssh://
+      - sftp://
+      - scp://
+      - others?
+- What happens if the remote connection isn't accessible to the user? Additional permissions necessary?    
+- Should support be limited to raw data first?
+- How should credentials be provided?
+      - environment variables
+      - SSH config / agent
+      - key file path
+      - password fallback
+- What should the expected behavior be for:
+      - exists()
+      - is_file()
+      - glob() / rglob()
+      - copying to local temp storage
+      - saving back to remote
+
+
+
+## Acceptance criteria
+
+  - A user can configure a remote raw-data directory and load supported raw files from it.
+  - Remote raw-file discovery works in a documented and tested way.
+  - Credential handling is documented and tested.
+  - Behavior for remote cellpy file loading/saving is explicitly supported or explicitly rejected with a clear error.
+  - The supported remote-path workflows are covered by tests and documented in the user docs.
+
+Notes
+
+  This issue is about remote path support as a feature. Refactoring the internal path abstraction should be treated as a separate issue unless it is
+  strictly necessary to complete this work.
+
+## Comments (curated summary)
+
+- **Clarifications / constraints**:
+  - Linked to / related work: jepegit/cellpy#371
+
+_Note: this section is an interpretive summary of the comment thread, not a verbatim dump. Source comments: 1, last comment by @jepegit on 2026-06-14._

cellpy-2.0.0a2/.issueflows/03-solved-issues/issue375_plan.md

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+# Plan: Issue #375 (+ #371) — Remote paths via `universal_pathlib`
+
+**Status:** Accepted (2026-07-17) — ready for `/iflow-start`.
+
+## Goal
+
+Ship usable remote raw/cellpy path workflows (`ssh`/`sftp`/`scp`) by replacing the Fabric-heavy `OtherPath` implementation with a thin cellpy API wrapper around [`universal_pathlib.UPath`](https://github.com/fsspec/universal_pathlib) (issue [#371](https://github.com/jepegit/cellpy/issues/371)), then documenting and testing the acceptance criteria from [#375](https://github.com/jepegit/cellpy/issues/375).
+
+This **combines #375 and #371** in one delivery: UPath is the remote backend *and* the way we get real `exists`/`is_file`/`glob`/copy semantics.
+
+## Constraints
+
+- **Preserve the cellpy `OtherPath` public surface** used by config, filefinder, loaders, and batch: `is_external`, `uri_prefix`, `location`, `original` / `full_path`, `raw_path`, `copy()` → local `pathlib.Path`, plus pathlib-like ops callers already use (`/`, `name`, `parent`, `glob`, `exists`, `is_file`, `is_dir`, …). Prefer delegation over rewriting call sites.
+- **Copy-then-load stays.** Instrument loaders and HDF5 still receive a **local** `pathlib.Path` after `OtherPath.copy()` / `resolve_hdf5_path` / `copy_to_temporary`. Do not teach readers remote open.
+- **URI / env back-compat:** `ssh://`, `sftp://`, `scp://` strings and `CELLPY_KEY_FILENAME` / `CELLPY_PASSWORD` (+ host/user where used) keep working; map into UPath/fsspec `storage_options` (Paramiko kwargs).
+- **Architecture G7 update:** Prior note said “keep Fabric OtherPath, fsspec later” ([`cellpy2-configuration-and-parameters-plan.md`](../../../architecture-plan/cellpy2-configuration-and-parameters-plan.md) §5b). **This work supersedes that:** wrap UPath now; keep a single external→local seam so backends can still change later. Record the decision in `.issueflows/04-designs-and-guides/` during `/iflow-start` (short note + link to #375/#371).
+- **No broad loader rewrite.** Touch other packages only where `isinstance(..., pathlib.Path)` / Fabric assumptions break.
+- **KISS:** One wrapper module; delete Fabric path helpers once tests pass; do not add S3/GCS/etc. product support in this issue even if UPath can open them.
+
+### Prior art
+
+| Hit | Role | Plan |
+| --- | --- | --- |
+| [`cellpy/internals/otherpath.py`](../../cellpy/internals/otherpath.py) | Fabric `OtherPathNew`/`Legacy`; stub external `exists`/`is_file` | **Replace guts** with UPath wrapper; drop dual New/Legacy if possible |
+| [#371 body sketch](https://github.com/jepegit/cellpy/issues/371) | Thin `OtherPath` → `_upath`; `copy` via `fs.get` | **Adopt** as implementation outline |
+| [`cellpy/internals/connections.py`](../../cellpy/internals/connections.py) | `OtherPath` export, `check_connection` | Retarget probe to UPath/`exists` or thin fs ping |
+| [`cellpy/readers/filefinder.py`](../../cellpy/readers/filefinder.py) | Remote discovery (SSH `find` / glob) | Prefer UPath `glob`/`iterdir`; remove Fabric `find` if redundant |
+| [`…/instruments/base.py`](../../cellpy/readers/instruments/base.py) `copy_to_temporary`, [`cellpy_file/read.py`](../../cellpy/readers/cellpy_file/read.py) `resolve_hdf5_path` | External → local | Keep call shape; ensure `OtherPath.copy()` still returns local `Path` |
+| [`cellpy_file/write.py`](../../cellpy/readers/cellpy_file/write.py) / `CellpyCell.save` | Local write | **Reject** remote save targets |
+| Config `OtherPathField` + `CELLPY_*` env | Path coercion / secrets | Wire credentials into UPath `storage_options`; docs |
+| [`tests/test_otherpaths.py`](../../tests/test_otherpaths.py) | Characterization + Fabric monkeypatches | **Expand first** (API contract), then retarget mocks to fsspec/UPath |
+| `isinstance(..., pathlib.Path)` call sites (`batch_journals`, `prmreader`, `config/types`, …) | Assume Path subclass | Audit + fix — UPath wrapper likely **not** a `pathlib.Path` subclass (#371 note) |
+| `fabric` in `pyproject.toml` | Current remote transport | **Remove** once UPath+Paramiko path is green (Paramiko already transitive / explicit) |
+| `universal-pathlib` | Not yet a dependency | **Add** (+ ensure `paramiko` for ssh/sftp) |
+
+## Approach
+
+### Product decisions (recommended)
+
+1. **Schemes in scope for “supported”:** `ssh://`, `sftp://`, and `scp://` (alias `scp` → `sftp`/`ssh` for UPath if needed). Other URI prefixes: either clear “not supported by cellpy” error **or** pass through to UPath only if zero extra deps — **default: supported set only** for documented workflows; unknown schemes raise clearly.
+2. **Auth:** `CELLPY_KEY_FILENAME` → Paramiko `key_filename`; `CELLPY_PASSWORD` → `password`; host/user from URI and/or `CELLPY_HOST`/`CELLPY_USER`. Document SSH agent / `~/.ssh/config` as Paramiko default behavior.
+3. **Unreachable remote:** Fail fast (no always-True stubs).
+4. **Cellpy files:** remote **read** via temp copy; remote **save** rejected with clear error.
+5. **`isinstance(x, pathlib.Path)`:** Prefer fixing call sites to accept `OtherPath` / `os.PathLike` / explicit conversion over pretending to subclass `pathlib.Path` (UPath’s model). Keep `isinstance(x, OtherPath)` working everywhere it already does.
+
+### Implementation order (matches #371 guidance)
+
+1. **Characterization tests** — lock current public `OtherPath` behavior (URI parse, properties, local ops, external `copy`/`glob` contracts, credential env errors) with mocks; note which tests encode Fabric-specific internals.
+2. **Add deps** — `universal-pathlib` (+ pin policy consistent with project); ensure `paramiko` available for ssh/sftp.
+3. **Rewrite `otherpath.py`** — thin wrapper around `UPath` preserving cellpy properties/methods; `_credentials_from_env()` → `storage_options`; `copy()` uses `fs.get` (or equivalent) to temp local path.
+4. **Call-site audit** — fix `isinstance(..., Path)` / pickle / pydantic `OtherPathField` / `check_connection` / filefinder remote search to work with wrapper (minimal diffs).
+5. **Remove Fabric path** — delete `_*_with_fabric` helpers; drop `fabric` dependency if nothing else needs it; simplify `get_otherpath_class()` (no 3.12 Legacy/New split if wrapper is version-agnostic).
+6. **#375 productization** — remote save rejection; user docs (URI, env, rawdatadir, temp-copy model, save policy); HISTORY note (backend change + truthful `exists`/`is_file`).
+7. **Close linkage** — PR references both #375 and #371; close #371 when merged (or mark duplicate of #375).
+
+### Out of scope
+
+- Product support for S3/HTTP/SMB/GCS as rawdatadir (even if UPath can open them)
+- Remote upload / save-back
+- Teaching instrument readers to open remote file handles
+- Full redesign of filefinder / batch path layout
+- Migrating Secrets into a new pydantic model beyond wiring env → `storage_options` (config plan Step 6 can refine later)
+
+### Scope / split check
+
+One issue-branch / one PR is the intent (user: combine with #371). Internally keep commits ordered: tests → wrapper → call sites → drop Fabric → docs. If the PR becomes unreviewable, split **docs/AC polish** only — do **not** ship Fabric hardening without UPath.
+
+## Files to touch
+
+| Path | Change |
+| --- | --- |
+| `pyproject.toml` / lock | Add `universal-pathlib`; drop `fabric` when unused; ensure `paramiko` |
+| `cellpy/internals/otherpath.py` | UPath-backed `OtherPath`; remove Fabric implementation |
+| `cellpy/internals/connections.py` | `check_connection` / exports |
+| `cellpy/readers/filefinder.py` | Discovery via UPath APIs; drop SSH `find` if obsolete |
+| `cellpy/readers/cellreader.py` and/or `cellpy_file/write.py` | Reject remote save |
+| `cellpy/config/types.py` (and related) | Coercion / isinstance fixes |
+| Other isinstance call sites (as found) | Accept `OtherPath` without requiring `pathlib.Path` subclass |
+| `tests/test_otherpaths.py` (+ filefinder / cell_readers as needed) | Contract tests; fsspec/UPath mocks |
+| `docs/source/…` | Remote path user docs |
+| `HISTORY.rst` (or project changelog) | User-visible notes |
+| `.issueflows/04-designs-and-guides/` | Short G7 decision: OtherPath wraps UPath |
+
+## Test strategy
+
+```bash
+uv run pytest tests/test_otherpaths.py -q
+uv run pytest tests/test_filefinder.py tests/test_cell_readers.py -q
+uv run pytest -m essential
+```
+
+- CI: mock fsspec/UPath filesystem (or monkeypatch `OtherPath._upath` / `fs.get`) — **no live SSH**.
+- Optional live tests remain env-gated (`CELLPY_TEST_*`).
+- Explicit tests: URI parse; env credentials → storage_options; external `exists`/`is_file` True/False; `copy` returns local `Path`; remote save raises; unsupported scheme error.
+
+## Open questions
+
+Confirm or revise:
+
+1. **Combine #371 into this branch/PR?**  
+   **Recommended (per your revise):** Yes — UPath first, then #375 ACs on top.
+
+2. **Drop `fabric` in the same PR?**  
+   **Recommended:** Yes, once tests pass on UPath+Paramiko.
+
+3. **`scp://` handling?**  
+   **Recommended:** Accept as alias to `sftp`/`ssh` for UPath (document alias).
+
+4. **Cellpy remote save?**  
+   **Recommended:** Reject with clear error (unchanged).
+
+5. **`isinstance(..., pathlib.Path)` strategy?**  
+   **Recommended:** Do **not** subclass `pathlib.Path`; fix call sites / use `OtherPath` or `PathLike` (matches #371 warning).
+
+6. **Docs?**  
+   **Recommended:** User-facing remote-paths section + HISTORY + design note under `04-designs-and-guides/`.
+
+7. **Close #371 how?**  
+   **Recommended:** Same PR `Closes #375` and `Closes #371` (or “Fixes #371 as part of #375”).
+
+---
+
+**Branch preflight (plan time):** `375-add-support-for-remote-paths-for-raw-data-and-cellpy-data-access`; sync with `origin/master` before `/iflow-start` as needed.

cellpy-2.0.0a2/.issueflows/03-solved-issues/issue375_status.md

@@ -0,0 +1,17 @@
+# Status: Issue #375 (+ #371)
+
+- [x] Done
+
+## What's done
+
+- Plan accepted; UPath-backed `OtherPath` (combines #371); Fabric removed.
+- Deps: `universal-pathlib`, `paramiko`; `fabric` dropped.
+- Truthful remote `exists` / `is_file` / `is_dir`; `scp://` → sftp; unsupported schemes error.
+- `check_connection` / `filefinder` on UPath; remote `CellpyCell.save` rejected.
+- Unit/mock tests + Docker SFTP property tests (`onlylocal`).
+- Docs: `remote_paths.md`, config link, `HISTORY.md`, G7 note `otherpath-upath.md`.
+- Essential + otherpaths/filefinder green at close.
+
+## Remaining work
+
+- None (landing via PR).

cellpy-2.0.0a2/.issueflows/04-designs-and-guides/otherpath-upath.md

@@ -0,0 +1,19 @@
+# OtherPath wraps universal_pathlib (G7)
+
+**Decision (issues #375 / #371):** `cellpy.internals.otherpath.OtherPath` is a thin
+compatibility wrapper around `upath.UPath` (fsspec backends). Remote raw/cellpy
+*reads* still go through a single external → local temp copy seam; loaders never
+speak SSH/SFTP.
+
+**Supersedes:** architecture-plan “keep Fabric OtherPath, revisit fsspec later”
+(configuration plan §5b, 2026-07-09). Fabric is removed once the wrapper is green.
+
+**Supported product schemes:** `ssh://`, `sftp://`, `scp://` (`scp` aliased to
+`sftp`). Other schemes are rejected with a clear error even if UPath could open them.
+
+**Credentials:** `CELLPY_KEY_FILENAME` / `CELLPY_PASSWORD` (and host/user env where
+used) map into fsspec/Paramiko `storage_options`. SSH agent / `~/.ssh/config` follow
+Paramiko defaults.
+
+**Not a `pathlib.Path` subclass:** call sites must accept `OtherPath` / `PathLike`
+explicitly; do not rely on `isinstance(x, pathlib.Path)`.

cellpy-2.0.0a2/.issueflows/04-designs-and-guides/release-procedure.md

@@ -0,0 +1,179 @@
+# Release procedure — GitHub release → PyPI
+
+**Context.** cellpy publishes to **PyPI as `cellpy`**. A published GitHub release
+triggers `.github/workflows/release.yml`: validate tag/branch → test → build →
+PyPI trusted publishing.
+
+**Authoritative companions (do not contradict these):**
+
+| Doc | Owns |
+|-----|------|
+| [`cellpy-v2-branching.md`](cellpy-v2-branching.md) | Branch layout after the 2026-07-16 flip |
+| `architecture-plan/cellpy2-release-and-branching-plan.md` (sibling repo) | Support matrix, cross-repo merge order (F9), final-legacy gates |
+| [`build-and-versioning.md`](build-and-versioning.md) | Tag-derived versioning (`uv-dynamic-versioning`) |
+
+> **Scheme (post-v1.1):** **`master` = v2 development**; **`v1.x` = 1.x
+> maintenance**. Old long-lived `v2` branch is retired — do not release from it.
+
+---
+
+## The moving parts
+
+- **Version** comes from the **git tag** via `uv-dynamic-versioning`. No
+  hand-edited `project.version`. Tag `vX.Y.Z` → PyPI `X.Y.Z`.
+- **Cut a release** with `gh release create --target <branch>`. CI checks that
+  the tagged commit is on that branch.
+- **`.github/workflows/release.yml`** on `release: published`:
+  - **validate** — `v1.*` on `origin/v1.x`; `v2.*` on `origin/master`; else fail
+  - **test** — `UV_NO_SOURCES=1 uv sync` → `pytest -m essential`
+  - **publish** — `uv build` → PyPI trusted publishing (`pypi` env)
+
+---
+
+## Which branch to release from
+
+| Tag pattern | Branch | PyPI channel |
+|-------------|--------|--------------|
+| `v1.x.y` / `v1.x.y.postN` | **`v1.x`** | stable |
+| `v1.x.yaN` / `bN` / `rcN` | **`v1.x`** | pre-release (`--pre`) |
+| `v2.0.0aN` / `bN` / `rcN` | **`master`** | pre-release only |
+| `v2.0.0` and later `v2.x.y` | **`master`** | stable |
+
+As of 2026-07-17: 1.x line at **`v1.1.0.post1`** on `v1.x`; v2 pre-releases from
+`master` (e.g. **`v2.0.0a1`**).
+
+---
+
+## Do this before any tag (hygiene)
+
+Releases tag **whatever commit is at HEAD**. Unrelated files on that commit ship
+with the release (and pollute `master` / `v1.x` history).
+
+1. **Be on the release branch**, not a feature branch.
+2. **`git status` must be empty** — no staged/unstaged changes **and no
+   untracked files**. Stray `.issueflows/01-current-issues/*` on `master` is a
+   common trap; those belong on the issue branch only.
+3. **Never `git add .` as release prep.** If you need a pin/HISTORY commit,
+   stage those paths explicitly.
+4. **Do not merge `master` into a feature branch** just to “get the release doc”
+   or move focus-issue files. Cherry-pick or recreate the file on the issue
+   branch instead.
+5. Prefer a **PR into the release line** for pin/HISTORY changes; direct pushes
+   to `master` bypass required checks (repo allows admin bypass — avoid it).
+
+---
+
+## Cutting a release (happy path)
+
+### A. 1.x maintenance (`v1.x`)
+
+```bash
+git switch v1.x && git pull --ff-only
+
+# Only if this release needs a pin / HISTORY commit — stage those files by name
+UV_NO_SOURCES=1 uv lock && UV_NO_SOURCES=1 uv sync
+uv run pytest          # full suite before a real 1.x ship
+
+git status             # must show a clean tree (no untracked)
+
+gh release create v1.1.1 --target v1.x --generate-notes
+
+gh run list --workflow release.yml --limit 1
+gh run watch <run-id>   # ID from first column; not the workflow filename
+```
+
+### B. v2 pre-release or stable (`master`)
+
+```bash
+git switch master && git pull --ff-only
+
+UV_NO_SOURCES=1 uv lock && UV_NO_SOURCES=1 uv sync
+uv run pytest -m essential   # full suite before v2.0.0 stable
+
+git status                   # must show a clean tree (no untracked)
+
+# Pre-release while v2 is unfinished:
+gh release create v2.0.0a2 --target master --generate-notes
+# Stable only when flip + gates are done:
+# gh release create v2.0.0 --target master --generate-notes
+
+gh run list --workflow release.yml --limit 1
+gh run watch <run-id>
+```
+
+**Optional:** check out the tag, `uv build`, inspect `dist/` metadata.
+
+### Failure modes
+
+- **Validate red (wrong branch):** delete the GitHub release **and** the tag;
+  recreate with the correct `--target`. Fix the tree first if the commit was wrong.
+- **Test job red:** fix on the release line, merge, cut a **new** tag — never reuse.
+- **Publish red but release exists:** PyPI may lack that version; ship the next tag.
+- **Accidental files in the tagged commit:** next patch/pre tag from a clean
+  commit; remove the stray paths on the release line via a normal PR (do not
+  rewrite published tags).
+
+---
+
+## Pre-release checklist (both lines)
+
+- [ ] On the **correct branch** (`v1.x` or `master`), not a feature branch.
+- [ ] `git status` clean — **including no untracked** issue-flow / scratch files.
+- [ ] Exact **`cellpycore==…`** pin for the release commit (see
+      `cellpy-v2-branching.md` for per-line policy).
+- [ ] `UV_NO_SOURCES=1 uv lock && UV_NO_SOURCES=1 uv sync`.
+- [ ] Release build does not depend on a local `[tool.uv.sources]` path.
+- [ ] Tests green (`-m essential` min; full suite before stable).
+- [ ] **`HISTORY.md`** updated.
+- [ ] Tag is **`vX.Y.Z`** (or `aN` / `bN` / `rcN` / `.postN` as appropriate).
+
+### Extra gates — final legacy 1.x ship
+
+Architecture plan §1 / §6.1 and
+`architecture-plan/cellpy-v103-vs-v104a3-observations.md`: CE /
+coulombic-difference, dropped columns, step classification must be intended
+**and** release-noted (or fixed). User notes:
+`architecture-plan/cellpy-v104-migration-notes.md`.
+
+### Extra gates — `v2.0.0` stable
+
+`cellpy-v2-branching.md` “At v2.0 release” + architecture release plan (support
+matrix, benchmarks, dependency budget). No stable 2.x until flip criteria pass.
+
+---
+
+## cellpy-core coordination (F9)
+
+**Additions:** core PR → core PyPI release → cellpy re-pin on the line → cellpy
+PR → cellpy GitHub release.
+
+**Removals:** cellpy migrates off first; then core deletes.
+
+After a core release a line needs:
+
+1. Bump `cellpycore` in that line’s `[project.dependencies]`
+2. `UV_NO_SOURCES=1 uv lock && UV_NO_SOURCES=1 uv sync`
+3. `uv run pytest -m essential`
+4. Merge, then include in the next cellpy release on that line
+
+`v1.x` stays on a conservative pin; `master` tracks newer core as v2 needs.
+See `cellpy-core` migration guide §2.
+
+---
+
+## One-time GitHub setup (maintainers)
+
+1. PyPI trusted publisher for `cellpy` → `jepegit/cellpy`, workflow `release.yml`,
+   environment `pypi`.
+2. Optional approval gate on the `pypi` environment.
+3. Branch protection on **`master`** and **`v1.x`** (`cellpy-v2-branching.md`).
+
+---
+
+## Tracking
+
+- Workflow: `.github/workflows/release.yml`
+- Branching: [`cellpy-v2-branching.md`](cellpy-v2-branching.md)
+- Build/versioning: [`build-and-versioning.md`](build-and-versioning.md)
+- Architecture: `architecture-plan/cellpy2-release-and-branching-plan.md`
+- Epic: [#402](https://github.com/jepegit/cellpy/issues/402)

{cellpy-2.0.0a1 → cellpy-2.0.0a2}/.issueflows/04-designs-and-guides/testing-and-coverage.md

@@ -45,10 +45,21 @@ The default `addopts` in `pyproject.toml` deselects slow/local/unfinished tests:
 
 ### Marker policy
 - `slowtest` - benchmarks and network/GitHub/cookiecutter pulls; deselected by default.
+- `onlylocal` - needs local resources (Docker SFTP for `tests/test_otherpaths_sftp.py`, live SSH, etc.); deselected by default `addopts`.
 - `skip(reason="only run locally")` - needs local resources (sftp, mdbtools, real raw data).
 - `skip(reason="...not needed in CI/CD...")` - downloads example data; run manually when needed.
 - `skip_on_macos` - macOS CI flakiness.
 - `xfail` - documents deprecated / not-implemented behavior; expected to fail.
+
+### Docker SFTP (`OtherPath`)
+
+```bash
+uv run pytest tests/test_otherpaths_sftp.py -m onlylocal
+```
+
+Uses `docker/sftp-test/compose.yml` (`atmoz/sftp` on `127.0.0.1:2223`). The
+session fixture starts/stops compose when the Docker daemon is up; otherwise
+the tests skip.
 - CI additionally `--ignore=tests/test_plotutils_summary_plot.py`; that file runs fine locally once
   the `[all]` extras (plotly/seaborn/kaleido) are installed.
 

{cellpy-2.0.0a1 → cellpy-2.0.0a2}/HISTORY.md

@@ -2,6 +2,14 @@
 
 ## [Unreleased]
 
+* Remote paths via `universal_pathlib` (#375, #371): `OtherPath` is now a thin
+  wrapper around `UPath` (fsspec/Paramiko) instead of Fabric. Supported schemes
+  remain `ssh://` / `sftp://` / `scp://` (scp aliased to sftp). Remote
+  `exists` / `is_file` / `is_dir` are truthful (no longer stubbed as always
+  true). Saving a cellpy file to a remote URI raises a clear error. Credentials
+  still come from `CELLPY_KEY_FILENAME` / `CELLPY_PASSWORD`. See
+  `docs/getting_started/remote_paths.md`.
+
 * Units are per-cell now (#427): `get_cellpy_units` returns a fresh
   `CellpyUnits` per call (optionally seeded from its argument, which used to
   be silently ignored), so changing units on one `CellpyCell` — directly, via

{cellpy-2.0.0a1 → cellpy-2.0.0a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellpy
-Version: 2.0.0a1
+Version: 2.0.0a2
 Summary: Extract and manipulate data from battery data testers.
 Project-URL: Homepage, https://github.com/jepegit/cellpy
 Project-URL: Repository, https://github.com/jepegit/cellpy
@@ -20,7 +20,6 @@ Requires-Dist: click
 Requires-Dist: cookiecutter
 Requires-Dist: dateparser
 Requires-Dist: defusedxml
-Requires-Dist: fabric
 Requires-Dist: ipykernel
 Requires-Dist: isal
 Requires-Dist: jinja2-time
@@ -28,6 +27,7 @@ Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: openpyxl
 Requires-Dist: pandas<4,>=3.0.3
+Requires-Dist: paramiko>=5.0.0
 Requires-Dist: pint
 Requires-Dist: platformdirs>=4.10.0
 Requires-Dist: polars
@@ -47,6 +47,7 @@ Requires-Dist: sqlalchemy>=2.0.0
 Requires-Dist: tables
 Requires-Dist: tqdm
 Requires-Dist: typer
+Requires-Dist: universal-pathlib>=0.3.10
 Requires-Dist: xmltodict
 Provides-Extra: all
 Requires-Dist: ipython; extra == 'all'

{cellpy-2.0.0a1 → cellpy-2.0.0a2}/cellpy/config/types.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import os
 from pathlib import Path
 from typing import Annotated, Any
 
@@ -33,6 +34,8 @@ OtherPathField = Annotated[
 def _coerce_path(value: Any) -> Path:
     if isinstance(value, Path):
         return value
+    if isinstance(value, OtherPath):
+        return Path(os.fspath(value))
     return Path(value)
 
 

cellpy-2.0.0a2/cellpy/internals/__init__.py

@@ -0,0 +1,11 @@
+"""Internal helpers (paths, lazy optional deps)."""
+
+# Kept for historical import compatibility; Fabric is no longer a dependency.
+from cellpy.libs.apipkg import initpkg
+
+initpkg(
+    __name__,
+    {
+        "externals": {},
+    },
+)

cellpy-2.0.0a2/cellpy/internals/connections.py

@@ -0,0 +1,116 @@
+"""Connection helpers and the public ``OtherPath`` export."""
+
+from __future__ import annotations
+
+import logging
+import os
+import pathlib
+import time
+from typing import Any, Dict, Optional, Union
+
+from cellpy.exceptions import UnderDefined
+from cellpy.internals.otherpath import (
+    ENV_VAR_CELLPY_KEY_FILENAME,
+    ENV_VAR_CELLPY_PASSWORD,
+    IMPLEMENTED_PROTOCOLS,
+    OtherPath,
+    URI_PREFIXES,
+    get_otherpath_class,
+)
+
+__all__ = [
+    "OtherPath",
+    "URI_PREFIXES",
+    "IMPLEMENTED_PROTOCOLS",
+    "ENV_VAR_CELLPY_KEY_FILENAME",
+    "ENV_VAR_CELLPY_PASSWORD",
+    "check_connection",
+    "get_otherpath_class",
+]
+
+
+def check_connection(
+    p: Optional[Union[str, pathlib.Path, OtherPath]] = None,
+) -> Dict[str, Any]:
+    """Probe a remote ``OtherPath`` (or configured ``rawdatadir``).
+
+    Uses UPath/fsspec instead of Fabric. Intended as a user-facing diagnostic.
+    """
+    logging.debug("checking connection")
+    if p is None:
+        print("No path given. Checking rawdatadir from prms.")
+        import cellpy.config as config
+
+        p = config.paths.rawdatadir
+
+    # Recreate so isinstance checks work even if the object crossed import boundaries.
+    p = OtherPath(p)
+    logging.debug("p: %s", p)
+
+    print("\nCollecting connection information:")
+
+    if not p.is_external:
+        print(f"   - {p} is not external. Returning.")
+        return {}
+
+    info: Dict[str, Any] = {
+        "is_external": p.is_external,
+        "uri_prefix": p.uri_prefix,
+        "location": p.location,
+        "raw_path": p.raw_path,
+        "full_path": p.full_path,
+        "host": p.location,
+    }
+
+    scheme = p.uri_prefix.replace("//", "")
+    info["uri_prefix"] = scheme
+    if scheme not in URI_PREFIXES:
+        print(f"   - uri_prefix {scheme} not recognized")
+    if scheme not in IMPLEMENTED_PROTOCOLS:
+        print(f"   - uri_prefix {scheme.replace(':', '')} not implemented yet")
+
+    password = os.getenv(ENV_VAR_CELLPY_PASSWORD, None)
+    info["password"] = "********" if password is not None else None
+
+    key_filename = os.getenv(ENV_VAR_CELLPY_KEY_FILENAME, None)
+    if password is None and key_filename is None:
+        print(
+            f"   - You must define either {ENV_VAR_CELLPY_PASSWORD} "
+            f"or {ENV_VAR_CELLPY_KEY_FILENAME} environment variables."
+        )
+    if key_filename is not None:
+        key_path = pathlib.Path(key_filename).expanduser().resolve()
+        info["key_filename"] = str(key_path)
+        if not key_path.is_file():
+            print(f"   - Could not find key file {key_path}")
+    else:
+        print("   - Using password")
+
+    for key, value in info.items():
+        print(f" {key}: {value}")
+
+    print("\nChecking connection:")
+    t0 = time.perf_counter()
+    try:
+        connect_kwargs, host = p.connection_info()
+        info["connect_kwargs_keys"] = sorted(connect_kwargs)
+        exists = p.exists()
+        print(f" exists()       [{time.perf_counter() - t0:.2f} seconds] {'OK' if exists else 'MISSING'}")
+        info["exists"] = exists
+        if exists and p.is_dir():
+            children = list(p.listdir(levels=0))
+            n_files = sum(1 for c in children if c.is_file())
+            n_dirs = sum(1 for c in children if c.is_dir())
+            info["number_of_files"] = n_files
+            info["number_of_sub_directories"] = n_dirs
+            print(f" listing        [{time.perf_counter() - t0:.2f} seconds] OK")
+            print(f" found {n_files} files and {n_dirs} sub directories")
+        elif not exists:
+            print(f"   - Path does not exist on {host}: {p.raw_path}")
+    except UnderDefined as exc:
+        print(f"   - UnderDefined: {exc}")
+    except Exception as exc:  # noqa: BLE001 - diagnostic helper should surface any failure
+        print(f"   - Could not connect to {p.location}")
+        print(f"     {exc}")
+
+    return info