Environments and environment views have taken over the role of `spack activate/deactivate`, and we should deprecate these commands for several reasons:
- Global activation is a really poor idea:
- Install prefixes should be immutable; since they can have multiple, unrelated dependents; see below
- Added complexity elsewhere: verification of installations, tarballs for build caches, creation of environment views of packages with unrelated extensions "globally activated"... by removing the feature, it gets easier for people to contribute, and we'd end up with fewer bugs due to edge cases.
- Environment accomplish the same thing for non-global "activation" i.e. `spack view`, but better.
Also we write in the docs:
```
However, Spack global activations have two potential drawbacks:
#. Activated packages that involve compiled C extensions may still
need their dependencies to be loaded manually. For example,
``spack load openblas`` might be required to make ``py-numpy``
work.
#. Global activations "break" a core feature of Spack, which is that
multiple versions of a package can co-exist side-by-side. For example,
suppose you wish to run a Python package in two different
environments but the same basic Python --- one with
``py-numpy@1.7`` and one with ``py-numpy@1.8``. Spack extensions
will not support this potential debugging use case.
```
Now that environments are established and views can take over the role of activation
non-destructively, we can remove global activation/deactivation.
* add version 1.7-20 to r-ade4
* add version 1.1-13 to r-adephylo
* add version 0.3-20 to r-adespatial
* add version 1.2-0 to r-afex
* add version 0.8-19 to r-amap
* add version 0.1.8 to r-aplot
* add version 2.0.8 to r-biasedurn
* add version 2.4-4 to r-bio3d
* add version 1.30.19 to r-biocmanager
* add version 1.2-9 to r-brobdingnag
* add version 0.4.1 to r-bslib
* add version 3.7.3 to r-callr
* add version 3.1-1 to r-car
* add version 0.3-62 to r-clue
* add version 1.2.0 to r-colourpicker
* add version 1.8.1 to r-commonmark
* add version 0.4.3 to r-cpp11
* add version 1.14.4 to r-data-table
* add version 1.34 to r-desolve
* add version 2.4.5 to r-devtools
* add version 0.6.30 to r-digest
* add version 0.26 to r-dt
* add version 1.7-12 to r-e1071
* add version 1.8.2 to r-emmeans
* add version 1.1.16 to r-exomedepth
* add version 0.1-8 to r-expint
* add version 0.4.0 to r-fontawesome
* add version 1.5-2 to r-fracdiff
* add version 1.10.0 to r-future-apply
* add version 3.0.1 to r-ggmap
* add version 3.4.0 to r-ggplot2
* add version 2.1.0 to r-ggraph
* add version 0.6.4 to r-ggsignif
* add version 0.6-7 to r-gmp
* add version 2022.10-2 to r-gparotation
* add version 0.8.3 to r-graphlayouts
* add version 1.8.8 to r-grbase
* add version 2.1-0 to r-gstat
* add version 0.18.6 to r-insight
* add version 1.3.1 to r-irkernel
* add version 1.8.3 to r-jsonlite
* add version 1.7.0 to r-lava
* add version 1.1-31 to r-lme4
* add version 5.6.17 to r-lpsolve
* add version 5.5.2.0-17.9 to r-lpsolveapi
* add version 1.2.9 to r-mapproj
* add version 3.4.1 to r-maps
* add version 1.1-5 to r-maptools
* add version 1.3 to r-markdown
* add version 6.0.0 to r-mclust
* add version 4.2-2 to r-memuse
* add version 1.8-41 to r-mgcv
* add version 1.2.5 to r-minqa
* add version 0.3.7 to r-nanotime
* add version 2.4.1.1 to r-nfactors
* add version 3.1-160 to r-nlme
* add version 2.7-1 to r-nmof
* add version 0.60-16 to r-np
* add version 2.0.4 to r-openssl
* add version 4.2.5.1 to r-openxlsx
* add version 0.3-8 to r-pbdzmq
* add version 2.0-3 to r-pcapp
* add version 0.7.0 to r-philentropy
* add version 2.0.3 to r-pkgcache
* add version 1.3.1 to r-pkgload
* add version 1.10-4 to r-polyclip
* add version 3.8.0 to r-processx
* add version 1.7.2 to r-ps
* add version 2.12.1 to r-r-utils
* add version 1.2.4 to r-ragg
* add version 3.7 to r-rainbow
* add version 0.0.20 to r-rcppannoy
* add version 0.3.3.9.3 to r-rcppeigen
* add version 0.3.12 to r-rcppgsl
* add version 1.0.2 to r-recipes
* add version 1.1.10 to r-rmutil
* add version 0.10.24 to r-rmysql
* add version 2.4.8 to r-rnexml
* add version 4.1.19 to r-rpart
* add version 1.7-2 to r-rrcov
* add version 0.8.28 to r-rsconnect
* add version 0.25 to r-servr
* add version 1.7.3 to r-shiny
* add version 3.0-0 to r-spatstat-data
* add version 3.0-3 to r-spatstat-geom
* add version 3.0-1 to r-spatstat-random
* add version 3.0-0 to r-spatstat-sparse
* add version 3.0-1 to r-spatstat-utils
* add version 1.8.0 to r-styler
* add version 3.4.1 to r-sys
* add version 1.5-2 to r-tclust
* add version 0.0.9 to r-tfmpvalue
* add version 1.2.0 to r-tidyselect
* add version 0.10-52 to r-tseries
* add version 4.2.2 to r-v8
* add version 0.5.0 to r-vctrs
* add version 2.6-4 to r-vegan
* add version 0.7.0 to r-wk
* add version 0.34 to r-xfun
* add version 1.0.6 to r-xlconnect
* add version 3.99-0.12 to r-xml
* add version 0.12.2 to r-xts
* add version 1.0-33 to r-yaimpute
* add version 2.3.6 to r-yaml
* add version 2.2.2 to r-zip
* add version 2.2-7 to r-deoptim
* add version 4.3.1 to r-ergm
* add version 0.18 to r-evaluate
* add version 1.29.0 to r-future
* add version 0.0.8 to r-ggfun
* add version 0.9.2 to r-ggrepel
* add version 1.9.0 to r-lubridate
* add version 4.10.1 to r-plotly
* add version 0.2.12 to r-rcppcctz
* add version 1.2 to r-rook
* add version 1.6-1 to r-segmented
* add version 4.2.1 to r-seurat
* add version 4.1.3 to r-seuratobject
* add version 1.0-9 to r-sf
* add version 1.5-1 to r-sp
* add version 1.8.1 to r-styler
* new package: r-timechange
* new package: r-stars
* new package: r-sftime
* new package: r-spatstat-explore
Co-authored-by: glennpj <glennpj@users.noreply.github.com>
* updates and fixes for libpressio
* differentiate between standalone and build tests
* add e4s tags
Co-authored-by: Robert Underwood <runderwood@anl.gov>
* include py-darshan
* include requested changes
* fix required versions
* fix style
* fix style
* Update package.py
* Update var/spack/repos/builtin/packages/py-darshan/package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
* Update package.py
Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>
Boost 1.64.0 has build errors when building the python and MPI modules. This was previously just a comment in the package.py which allowed broken specs to concretize. The comments are now expressed in conflicts to prevent this.
Currently, external `PythonPackage`s cause install failures because the logic in `PythonPackage` assumes that it can ask for `spec["python"]`. Because we chop off externals' dependencies, an external Python extension may not have a `python` dependency.
This PR resolves the issue by guaranteeing that a `python` node is present in one of two ways:
1. If there is already a `python` node in the DAG, we wire the external up to it.
2. If there is no existing `python` node, we wire up a synthetic external `python` node, and we assume that it has the same prefix as the external.
The assumption in (2) isn't always valid, but it's better than leaving the user with a non-working `PythonPackage`.
The logic here is specific to `python`, but other types of extensions could take advantage of it. Packages need only define `update_external_dependencies(self)`, and this method will be called on externals after concretization. This likely needs to be fleshed out in the future so that any added nodes are included in concretization, but for now we only bolt on dependencies post-concretization.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
