Clean up (#1009)

C2SM · Oct 25, 2024 · 5302b86 · 5302b86
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diff --git a/Jenkinsfile b/Jenkinsfile
@@ -30,6 +30,7 @@ pipeline {
                         }
                     }
                     stage('Bootstrap spack') {
+                        // Bootstrapping spack is a separate stage to avoid problems with concurrently bootstrapping spack in the tests.
                         steps {
                             sh """
                             source env/bin/activate

diff --git a/README.md b/README.md
@@ -66,11 +66,11 @@ After an update we advice to rebuild packages, preferably in a new shell so that
 |  | Command |
 | --- | --- |
 | Clone | `git clone --depth 1 --recurse-submodules --shallow-submodules -b <branch/tag> https://github.com/C2SM/spack-c2sm.git` |
-| Load | `. spack-c2sm/setup-env.sh` autodetects machine <br>or<br>`. spack-c2sm/setup-env.sh <machine>` forces machine<br>or<br>`. spack-c2sm/setup-env.sh unknown` uses blank config<br>`spack compiler find` [autodetects compilers](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-compiler-find)<br>`spack external find --all` [autodetects externally installed packages](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-external-find)|
 | Update | `git pull`<br>`git submodule update --recursive` |
-| Clean | `spack uninstall -a` [uninstalls all packages](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-uninstall)<br>`spack clean -a` [cleans all misc caches](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-clean)<br>`rm -rf ~/.spack` removes user scope data |
+| Load | `. spack-c2sm/setup-env.sh` to run without an upstream<br>or<br>`. spack-c2sm/setup-env.sh /user-environment` to use `/user-environment` as an upsream<br>`spack compiler find` [autodetects compilers](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-compiler-find)<br>`spack external find --all` [autodetects externally installed packages](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-external-find)|
+| Clean | `spack uninstall -a` [uninstalls all packages](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-uninstall)<br>`spack clean -a` [cleans all misc caches](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-clean)|
 
-[**Spec syntax**](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#specs-dependencies): `<package>`[`@<version>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#version-specifier)[`%<compiler>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#compiler-specifier)[`+<variant> ~<variant>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#variants)[`^<sub-package> +<sub-package-variant>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#specs-dependencies)[`<compiler flags>`](https://spack.readthedocs.io/en/v0.18.1/basic_usage.html#compiler-flags)
+[**Spec syntax**](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#specs-dependencies): `<package>`[`@<version>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#version-specifier)[`%<compiler>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#compiler-specifier)[`+<variant> ~<variant>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#variants)[`^<sub-package> +<sub-package-variant>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#specs-dependencies)[`<compiler flags>`](https://spack.readthedocs.io/en/v0.21.1/basic_usage.html#compiler-flags)
 
 |  | Command |
 | --- | --- |
@@ -79,7 +79,7 @@ After an update we advice to rebuild packages, preferably in a new shell so that
 | Spec | `spack spec <spec>` concretizes abstract spec (unspecfied variant = **any**)<br>*Spack is not required to use the default of an unspecified variant. The default value is only a tiebreaker for the concretizer.* |
 | Install  | `spack install <spec>` |
 | Locate | `spack location --install-dir <spec>` prints location of **all** installs that satisfy the spec |
-| [Load env](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-load) | `spack load <spec>` loads run environment |
-| [Activate env](https://spack.readthedocs.io/en/v0.18.1/environments.html) | `spack env activate <env_name>` |
-| [Deactivate env](https://spack.readthedocs.io/en/v0.18.1/environments.html) | `spack deactivate` |
+| [Load env](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-load) | `spack load <spec>` loads run environment |
+| [Activate env](https://spack.readthedocs.io/en/v0.21.1/environments.html) | `spack env activate <env_name>` |
+| [Deactivate env](https://spack.readthedocs.io/en/v0.21.1/environments.html) | `spack deactivate` |
 
diff --git a/docs/InstanceManagement.rst b/docs/InstanceManagement.rst
@@ -17,7 +17,7 @@ Versions
 
 Generally, we recommend to host a released version of spack-c2sm and upgrade to newer versions when you see fit.
 But if you fancy the latest developments before they are released, you may follow the branch ``main``.
-For automated systems that regularly set up a new Spack instance, using a fixed version and updating on demand, is more robust and limits the dependencies of your project. Following ``main`` on the other hand automatically updates to the newest features but breaks upon API chaning commits in spack-c2sm.
+For automated systems that regularly set up a new Spack instance, using a fixed version and updating on demand, is more robust and limits the dependencies of your project. Following ``main`` on the other hand automatically updates to the newest features but breaks upon API changing commits in spack-c2sm.
 
 Create a new Spack instance
 ---------------------------
@@ -29,20 +29,13 @@ To get an instance, clone spack-c2sm and its submodule spack.
     $ git clone --depth 1 --recurse-submodules --shallow-submodules -b <branch/tag> https://github.com/C2SM/spack-c2sm.git
 
 The arguments ``--depth 1`` and ``--shallow-submodules`` are optional, but they reduce the amount of downloaded data.
-It is recommended to clone ``spack-c2sm`` in a location that does **not** undergo a
-regular cleanup.
+It is recommended to clone ``spack-c2sm`` in a location that does **not** undergo a regular cleanup.
 
 Setup Spack environment
 -----------------------
 
-``setup-env.sh`` automatically detects the machine it is running on, or falls back to a generic configuration called 'unknown'.
-``setup-env.sh <machine>`` forces a machine. This also works with 'unknown' as a machine, which is useful in a container.
-It prints which machine it detected.
-You may simply execute
-
-.. code-block:: console
-
-    $ . spack-c2sm/setup-env.sh
+``setup-env.sh <upstream>`` loads spack with the provided upstream to look for preinstalled software and configurations.
+``setup-env.sh`` loads spack without an upstream.
 
 
 Update Spack instance
@@ -61,10 +54,9 @@ This is required after upgrades at CSCS or if you need new features of a package
 Clean Spack instance
 --------------------
 
-To clean a Spack instance, empty the caches, uninstall everything and remove misc caches:
+To clean a Spack instance, empty the caches and uninstall everything:
 
 .. code-block:: console
 
-    $ spack clean -a #[cleans all misc caches](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-clean)
-    $ spack uninstall -a #[uninstalls all packages](https://spack.readthedocs.io/en/v0.18.1/command_index.html?highlight=spack%20load#spack-uninstall)
-    $ rm -rf ~/.spack #removes user scope data
+    $ spack clean -a #[cleans all misc caches](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-clean)
+    $ spack uninstall -a #[uninstalls all packages](https://spack.readthedocs.io/en/v0.21.1/command_index.html?highlight=spack%20load#spack-uninstall)
diff --git a/docs/UpstreamManagement.rst b/docs/UpstreamManagement.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -20,7 +20,6 @@ and deploy our software on supercomputers, mostly at the
    InstanceManagement
    SpackCommands
    Testing
-   UpstreamManagement
    CodeDevelopment
    SpackChoice
 
diff --git a/requirements.txt b/requirements.txt
@@ -1,2 +1 @@
-requests
 pytest-xdist
diff --git a/src/__init__.py b/src/__init__.py
diff --git a/src/machine.py b/src/machine.py
diff --git a/src/machine.sh b/src/machine.sh
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,6 +30,7 @@ pipeline { @@
                             }
                         }
                         stage('Bootstrap spack') {
+                            // Bootstrapping spack is a separate stage to avoid problems with concurrently bootstrapping spack in the tests.
                             steps {
                                 sh """
                                 source env/bin/activate
@@ Expand Down @@