Merge pull request #305 from easybuilders/develop

release EasyBuild v5.0.0

Author: branfosj

.github/workflows/deploy.yml

@@ -11,17 +11,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
         with:
           fetch-depth: 0
 
       - name: set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: '3.10'
 
       - name: checkout easybuild framework
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
         with:
           repository: easybuilders/easybuild-framework
           path: src/easybuild-framework

.github/workflows/flake8.yml

@@ -8,12 +8,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
       - name: set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: '3.10'
 
       - name: flake8 Lint
-        uses: py-actions/flake8@v2
+        uses: py-actions/flake8@84ec6726560b6d5bd68f2a5bed83d62b52bb50ba # v2.3.0

.github/workflows/markdown-linting.yml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
 
       - name: MarkdownLint
-        uses: DavidAnson/markdownlint-cli2-action@v10
+        uses: DavidAnson/markdownlint-cli2-action@05f32210e84442804257b2a6f20b273450ec8265 # v19.1.0
         with:
           # all markdown, except filter out {demos,version-specific}/* for now, until we fix issues in those sections
           globs: |

.github/workflows/test.yml

@@ -9,17 +9,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
+
         with:
           fetch-depth: 0
 
       - name: set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0
         with:
           python-version: '3.10'
 
       - name: Codespell action
-        uses: codespell-project/actions-codespell@master
+        uses: codespell-project/actions-codespell@406322ec52dd7b488e48c1c4b82e2a8b3a1bf630 # v2.1
         with:
           check_filenames: true
           ignore_words_list: atleast,ninjs,simpy,proovread,namd,precice,crate,ake
@@ -32,7 +33,7 @@ jobs:
         run: python ./.github/workflows/link_check.py
 
       - name: checkout easybuild framework
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
         with:
           repository: easybuilders/easybuild-framework
           path: src/easybuild-framework
@@ -43,7 +44,7 @@ jobs:
           pip install -r requirements.txt
           mkdocs --version
 
-      - name: build tutorial
+      - name: build docs
         # can't use --strict due to warnings being produced by mkdocs-redirect plugin
         # because we are re-directing .html pages
         # run: mkdocs build --strict

.github/workflows/yamllint.yml

@@ -7,8 +7,8 @@ jobs:
   lintAllTheThings:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # 4.2.2
       - name: yaml-lint
-        uses: ibiqlik/action-yamllint@v3
+        uses: ibiqlik/action-yamllint@2576378a8e339169678f9939646ee3ee325e845c # v3.1.1
         with:
           config_file: .yamllint.yml

docs/api/index.md

@@ -37,7 +37,7 @@ This includes (but is not limited to):
 - **some functionality has been deprecated**, including the use of the `run_cmd` and `run_cmd_qa` functions (`run_shell_cmd` should be used instead);
 - easyconfigs using an old [unsupported toolchain](../policies/toolchains.md) have been moved to the [easyconfigs archive](https://github.com/easybuilders/easybuild-easyconfigs-archive);
 
-## Installation
+## Installation {: #eb5.0.0beta1_installation }
 
 To install the initial beta release of EasyBuild v5.0.0 (`5.0.0beta1`), you can either:
 

docs/easybuild-v5/5.0.0beta1.md

@@ -0,0 +1,209 @@
+# Changed default configuration or behaviour in EasyBuild v5.0
+
+*(for a full overview of changes in EasyBuild v5.0, see [here](index.md))*
+
+The default value for several EasyBuild configuration settings has been changed in EasyBuild v5.0.
+
+**Changed default configuration in EasyBuild framework**
+
+- [RPATH linking is enabled by default (`--rpath`)][path]
+- [Trace output is enabled by default (`--trace`)][trace)]
+- [Including `extensions` statement in generated modules is enabled by default (`--module-extensions`)][module-extensions]
+- [Using `depends_on` for dependencies in generated modules is enabled by default (`module-depends-on`)][module-depends-on]
+- [Use Slurm as default job backend (`--job-backend`)][job-backend]
+- [Default maximum build parallelism is set to 16 (`--max-parallel`)][max-parallel-16]
+
+**Changed behaviour in EasyBuild framework**
+
+- [Change semantics of `--dry-run` (`-D`), so it doesn't imply `--robot` (`-r`)][dry-run-robot]
+- [Move verifying of checksums from `source` to `fetch` step, to include it with `--fetch`][verifying-checksums]
+- [Create `lib` to `lib64` symlink (and vice versa) *before* running `postinstallcmds`][lib-lib64-symlink]
+- [Use `sha256` as the default checksum type][sha256]
+- [Use default value `$XDG_CONFIG_DIRS` from XDG basedir spec: `/etc/xdg` (instead of `/etc`)][XDG_CONFIG_DIRS_default]
+- [Reverse order for parsing files in `$XDG_CONFIG_DIRS`][XDG_CONFIG_DIRS_order]
+- [Don't allow unresolved templates in easyconfig parameters by default][unresolved-templates]
+- [Refactor `make_extension_string` method in `EasyBlock` class][make_extension_string]
+- [Change default for `change_into_dir` option in `extract_file` function to to `False`][extract_file]
+- [Change `Toolchain.get_flag` so it doesn't automatically prepend a dash (`-`) to compiler][toolchain-get-flag-dash]
+- [Enforce correct `.patch(.*)` extension for patch files][patch-extension]
+- [Run sanity checks commands from an empty temporary directory rather than the software install directory][sanity-check-commands]
+- [Only allow use of `rpath` toolchain option when `system` toolchain is used][system-toolchain-options]
+
+**Changed defaults in easyblocks**
+
+- [`download_dep_fail`, `use_pip`, `sanity_pip_check` are enabled by default for Python package installations][python-pkgs-defaults]
+- [`CMakeMake` easyblock sets `LIBDIR` configuration option to `lib` by default][cmakemake-libdir]
+
+---
+
+## RPATH linking is enabled by default (`--rpath`) {: #rpath }
+
+[RPATH linking][rpath_support] is enabled by default in EasyBuild v5.0.
+
+The benefits for enabling RPATH are explained in [Why RPATH?][rpath_support_why].
+
+This enhancement **does not** add any filtering of environment variables. This means `$LD_LIBRARY_PATH`
+will continue to be appended by the environment module files EasyBuild generates,
+unless it is configured to filter these variables (via `--filter-env-vars`,
+see also [Relation to `$LD_LIBRARY_PATH`][rpath_support_LD_LIBRARY_PATH]).
+
+The RPATH part of the EasyBuild sanity check has been relaxed (by default,
+to allow for installing software that uses RPATH linking on top of existing software installations that do not use RPATH.
+The RPATH sanity check can be made strict again via the `strict-rpath-sanity-check` EasyBuild configuration setting.
+
+To disable RPATH linking, either:
+
+- Use the `--disable-rpath` command line option;
+- Set the `$EASYBUILD_DISABLE_RPATH` environment variable;
+- Disable RPATH linking in an EasyBuild [configuration file](../configuration.md#configuration_file):
+
+    ``` ini
+    [override]
+    rpath=0
+    ```
+
+---
+
+## Trace output is enabled by default (`--trace`) {: #trace }
+
+The [`--trace` option](../tracing-progress.md) is enabled by default.
+
+This makes the output produced by the `eb` command more informative, by providing more information about what's going on in the background.
+
+To disable trace output, either:
+
+- Use the `--disable-trace` command line option;
+- Set the `$EASYBUILD_DISABLE_TRACE` environment variable;
+- Disable trace mode in a [configuration file](../configuration.md#configuration_file):
+
+    ``` ini
+    [override]
+    trace=0
+    ```
+
+---
+
+## Including `extensions` statement in generated modules is enabled by default (`module-extensions`) {: #module-extensions }
+
+*(more info soon)*
+
+---
+
+## Using `depends_on` for dependencies in generated modules is enabled by default (`module-depends-on`) {: #module-depends-on }
+
+*(more info soon)*
+
+---
+
+## Use Slurm as default job backend (`job-backend`) {: #job-backend }
+
+*(more info soon)*
+
+
+---
+
+## Default maximum build parallelism is set to 16 (`max-parallel`) {: #max-parallel-16 }
+
+*(more info soon, ideally including some "scaling" data for long-running builds like GCC, LLVM, OpenFOAM, ...)*
+
+---
+
+## Change semantics of `--dry-run` (`-D`), so it doesn't imply `--robot` (`-r`) {: #dry-run-robot }
+
+*(more info soon)*
+
+---
+
+## Move verifying of checksums from `source` to `fetch` step, to include it with `--fetch` {: #verifying-checksums }
+
+*(more info soon)*
+
+---
+
+## Create `lib` to `lib64` symlink (and vice versa) *before* running `postinstallcmds` {: #lib-lib64-symlink }
+
+*(more info soon)*
+
+---
+
+## Use `sha256` as the default checksum type {: #sha256 }
+
+The default checksum type, used in EasyConfigs, is now set to `sha256`.
+
+We have also [deprecated the older checksums types](deprecated-functionality.md#checksums).
+
+---
+
+## Use default value `$XDG_CONFIG_DIRS` from XDG basedir spec: `/etc/xdg` (instead of `/etc`) {: #XDG_CONFIG_DIRS_default }
+
+*(more info soon)*
+
+---
+
+
+## Reverse order for parsing files in `$XDG_CONFIG_DIRS` {: #XDG_CONFIG_DIRS_order }
+
+*(more info soon)*
+
+---
+
+## Don't allow unresolved templates in easyconfig parameters by default {: #unresolved-templates }
+
+*(more info soon, incl. support for `allow-unresolved-templates` configuration setting)*
+
+---
+
+## Refactor `make_extension_string` method in `EasyBlock` class {: #make_extension_string }
+
+*(more info soon)*
+
+---
+
+## Change default for `change_into_dir` option in `extract_file` function to to `False` {: #extract_file }
+
+*(more info soon)*
+
+---
+
+
+## Change `Toolchain.get_flag` so it doesn't automatically prepend a dash (`-`) to compiler {: #toolchain-get-flag-dash }
+
+*(more info soon)*
+
+---
+
+## Enforce correct `.patch(.*)` extension for patch files {: #changes.md#patch-extension }
+
+*(more info soon)*
+
+---
+
+
+## Run sanity checks commands from an empty temporary directory rather than the software install directory { : #sanity-check-commands }
+
+*(more info soon)*
+
+---
+
+## Only allow use of `rpath` toolchain option when `system` toolchain is used {: #system-toolchain-options }
+
+*(more info soon)*
+
+---
+
+## `download_dep_fail`, `use_pip`, `sanity_pip_check` are enabled by default for Python package installations { : #python-pkgs-defaults }
+
+The `download_dep_fail`, `use_pip`, and `sanity_pip_check` easyconfig parameters are now enabled by default
+in the `PythonPackage` and `PythonBundle` generic easyblocks (and the easyblocks that derive from them).
+
+This means that these should no longer be explicitly set to `True` in easyconfig files using these easyblocks.
+
+---
+
+## `CMakeMake` easyblock sets `LIBDIR` configuration option to `lib` by default { : #cmakemake-libdir }
+
+The generic `CMakeMake` easyblock will use `-DCMAKE_INSTALL_LIBDIR=lib` by default as option to the `cmake` command.
+Easyconfig files that specify this via `configopts` should be adjusted accordingly.
+
+A custom easyconfig parameter named `install_libdir` has been added to `CMakeMake` to specify a custom value should that
+be required.