* freeimage: fails to compile with c++17, use c++14
Only `opencascade` when a (non-default) variant depends on `freeimage`, which seems to have gone unmaintained. There are c++17 standard violations [[1]]( https://en.cppreference.com/w/cpp/language/except_spec) in the code, so we can at most expect c++14. Since some compilers default to c++17 (gcc-12) we need to be explicit.
* freeimage: install directly in prefix
* freeimage: fix inverted patch
* environments: don't rewrite relative view path, expand path on cli ahead of time
Currently if you have a spack.yaml that specifies a view by relative
path, Spack expands it to an absolute path on `spack -e . install` and
persists that to disk.
This is rather annoying when you have a `spack.yaml` file inside a git
repo, cause you want to use relative paths to make it relocatable, but
you constantly have to undo the changes made to spack.yaml by Spack.
So, as an alternative:
1. Always stick to paths as they are provided in spack.yaml, never
replace them with a canonicalized version
2. Turn relative paths on the command line into absolute paths before
storing to spack.yaml. This way you can do `spack env create --dir
./env --with-view ./view` and both `./env` and `./view` are resolved
to the current working dir, as expected (not `./env/view`). This
corresponds to the old behavior of `spack env create`.
* create --with-view always takes a value
All packages with explicit Windows support can be found with
`spack list --tags=windows`.
This also removes the documentation which explicitly lists
supported packages on Windows (which is currently out of date and
is now unnecessary with the added tags).
Note that if a package does not appear in this list, it *may*
still build on Windows, but it likely means that no explicit
attempt has been made to support it.
* nextflow recipe: added latest stable version
* tower-cli recipe: added latest release
* recipes tower-agent and tower-cli renamed to nf-tower-agent and nf-tower-cli
* recipes nf-tower-agent and nf-tower-cli: small fix
* nf-core-tools recipe: added most py- dependencies
* nf-core-tools: recipe without galaxy-tool-util (for testing)
* fixed typos in py-yacman recipe
* fixed typos in py-pytest-workflow recipe
* fixed typo in nf-core-tools recipe
* fixed typos in py-yacman recipe
* fixes in recipes for py-questionary and py-url-normalize
* fixes to py-yacman recipe
* style fixes to py- packages that are dependencies to nf-core-tools
* fix in py-requests-cache recipe
* added missing dep in py-requests-cache recipe
* nf-core-tools deps: removed redundant python dep for py packages oyaml and piper
* nf-core-tools recipe: final, incl dep on py-galaxy-tool-util
* nf-core-tools: new version with extra dependency
* added py-galaxy-util, draft: added some required dep versions, still have to add 40+ deps
* nextflow and nf-core-tools packages: added my self as maintainer
* style fixes
* style fix for nf-core-tools recipe
* added license to py-logmuse recipe
* audit fixes
* style fix after audit fix
* py-galaxy-tool-util: added deps 1st bunch
* audit/style fixes, including adding missing dep package
* more audit/style fixes
* more more audit/style fixes
* moooore audit fixes
* py-galaxy-tool-util: dependencies 2nd chunk
* silly audit fix
* py-galaxy-util deps: 3rd bunch - first 20 done
* fixes
* style fix
* py-galaxy-tool-util: 4th bunch of deps
* stashing dep recipe backbones for py-galaxy-tool-util
* nf-core-tools: using pre-built wheel for dependency py-galaxy-tool-util
* nf-core-tools: adding also py-galaxy-util, as wheel
* fix
* nextflow: added latest bugfix version
* Update var/spack/repos/builtin/packages/nf-core-tools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/nf-core-tools/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* nf-core-tools pr: 1st bunch of review edits
* nf-core-tools: 2nd bunch of review edits
* adding back tower-agent and tower-cli as deprecated
* nf-core-tools: 3rd bunch of review edits
* small style fix
* prepping py-galaxy-tool-util for further work
* nf-core-tools: last bunch of deps, except for galaxy-tool-util and pulsar
* audit fixes
* updates to py-galaxy-tool-util and its deps, still 2 to work on
* one style fix
* updated recipe for py-galaxy-util
* updated recipe for py-pulsar-galaxy-lib
* typo fix
* shasum fixes
* updated py-sqlalchemy from develop
* added newest versions (today) for nf-tower-agent and nf-tower-cli
* Update var/spack/repos/builtin/packages/py-requests-cache/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-requests-cache/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* adding 2nd bunch of nf-core deps from update/nextflow-tools
* adding 3rd bunch of nf-core deps from update/nextflow-tools
* 4th chunk of nf-core deps from update/nextflow-tools
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pastedeploy/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-pebble/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-gunicorn/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-starlette/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-parsley/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-paste/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-paste/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* py-gxformat2: added comment
* py-lagom: now using github tarballs
* fix for py-lagom
* adding missing deps to py-fastapi-utils
* another fix to py-lagom
* Update var/spack/repos/builtin/packages/py-dnspython/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-fastapi-utils/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-lagom/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-supervisor/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update var/spack/repos/builtin/packages/py-social-auth-core/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fixes from PR review
* adding missing deps, from PR review
* py-galaxy2cwl from github tarball, as per PR review
* fix to py-tuswsgi, as per PR review
* nf-tools: edits from PR review
* adding 3x more galaxy deps
* fix
* fixing circular dep of py-poetry-plugin-export with py-poetry
* added newest nf-core-tools version
* Update var/spack/repos/builtin/packages/py-galaxy-util/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* fix in py-poetry-plugin-export
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Currently, the `python` package tries to set `CPATH` in `setup_run_environment()`.
We no longer set `CPATH` and other destructive environment variables (like
`LD_LIBRARY_PATH`) in modules, so we shouldn't do something special for Python.
Also, the way `python` sets `CPATH` causes issues. Because it does a header search to
find directories containing headers, if you bootstrap `mypy` or other style tools on a
fresh Ubuntu image with *no* python devel headers installed, you'll get an error like
this when trying to load the thing you just installed:
```console
[root@980de539843d /]# spack -b load py-mypy
==> Error: Unable to locate python headers in any of these locations:
/usr/include/python3.6m
/usr/include/3.6
/usr/Headers
```
The headers and includes aren't needed to get `mypy` in the path or for `mypy` to work,
so we're failing unnecessarily here.
- [x] remove `setup_run_environment()` from `python/package.py`
Since SPACK_PACKAGE_IDS is now also "namespaced" with <prefix>, it makes
more sense to call the flag `--make-prefix` and alias the old flag
`--make-target-prefix` to it.
