ccpem-pipeliner 1.6.0__tar.gz

ccpem_pipeliner-1.6.0/LICENSE

@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.

ccpem_pipeliner-1.6.0/PKG-INFO

@@ -0,0 +1,176 @@
+Metadata-Version: 2.4
+Name: ccpem-pipeliner
+Version: 1.6.0
+Summary: CCP-EM Pipeliner
+License-Expression: MPL-2.0
+Project-URL: Repository, https://gitlab.com/ccpem/ccpem-pipeliner
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ccpem-utils==0.0.1.dev34
+Requires-Dist: gemmi==0.7.4
+Requires-Dist: importlib-metadata>=3.6.0
+Requires-Dist: matplotlib
+Requires-Dist: mrcfile
+Requires-Dist: numpy>=2.0.2
+Requires-Dist: pandas
+Requires-Dist: Pillow>=11.3.0
+Requires-Dist: plotly
+Requires-Dist: pyyaml
+Requires-Dist: requests
+Requires-Dist: scipy>=1.13.1
+Requires-Dist: imodmodel
+Requires-Dist: pdbe-mmcif-validator==0.1.92
+Provides-Extra: dev
+Requires-Dist: black==25.11.0; extra == "dev"
+Requires-Dist: flake8==7.3.0; extra == "dev"
+Requires-Dist: mypy==1.19.1; extra == "dev"
+Requires-Dist: flake8-pyproject; extra == "dev"
+Requires-Dist: pandas-stubs; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: sniffio; extra == "dev"
+Requires-Dist: types-pillow; extra == "dev"
+Requires-Dist: types-setuptools; extra == "dev"
+Requires-Dist: types-pyyaml; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: myst-parser; extra == "docs"
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-argparse; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Dynamic: license-file
+
+# CCPEM-pipeliner
+
+[![Documentation](https://readthedocs.org/projects/ccpem-pipeliner/badge/ "Documentation on ReadTheDocs")](https://ccpem-pipeliner.readthedocs.io/)
+
+![ccpem-pipeliner header image](docs/source/header.png)
+
+The CCP-EM-pipeliner is a Python library which provides the ‘business logic’ layer for 
+the CCP-EM software suite (v2). It can be used separately and is open source 
+(MPL 2.0). 
+
+Pipeliner provides command line functionality to:
+
+- Run image processing tasks (jobs)
+- Continue/overwrite existing jobs
+- Create scripts for automated workflows
+- Cleanup to remove tmp/unneeded files
+- Create archives to preserve workflows
+- Generate metadata reports
+- Generate literature reference lists
+- Generate results for viewing in the CCP-EM Doppio GUI 
+
+CCP-EM pipeliner allows the design of custom, automated cryoEM workflows for SPA, STA 
+and model building and is used as part of eBIC/DLS’s automated processing pipeliner 
+and the CZII CryoET Object Identification Kaggle challenge. 
+
+It produces Doppio (or RELION) projects which can be viewed and continued in the UI.
+Project created in pipeliner are fully compatible with projects 
+created using the RELION GUI.
+
+
+## Installation
+
+Install from PyPI with ``pip install ccpem-pipeliner``
+
+To install the package from source navigate into the `ccpem-pipeliner` directory and
+install the pipeliner with the command:
+
+``pip install -e .``
+
+## Check the installation
+
+Once the pipeliner is installed use the command `pipeliner.check_setup` to check that
+the setup is complete and the pipeliner can find the Relion programs it needs to run.
+
+## Documentation
+
+Documentation is available online at:
+[ccpem-pipeliner.readthedocs.io/en/latest/](https://ccpem-pipeliner.readthedocs.io/en/latest/)
+
+To build the documentation yourself, install the documentation build requirements
+as follows:
+
+`pip install -e .[docs]`
+
+Then navigate to the `ccpem-pipeliner/docs` directory and run the command:
+
+`make html`
+
+Then open the file `ccpem-pipeliner/docs/_build/html/index.html` in a web browser to access the
+documentation.
+
+## Adding plugins
+
+To add additional job plugins the plugin must first be written as a `PipelinerJob` object.
+See the [pipeliner documentation](https://ccpem-pipeliner.readthedocs.io/en/latest/source/pipeliner_jobs.html)
+for a description of the format.
+
+The plugin must then be placed in the `Pipeliner/jobs/` folder or one of its subfolders, or create a new subfolder.
+
+Once the plugin file is in place add it to the list of entry points in `pyproject.toml`.
+
+If `pyproject.toml` has been modified update the pipeliner by running `pip install -e .` for the changes to
+take effect.
+
+## For Developers
+
+It's a good idea to work in a virtual environment for this project. Set one up as
+follows:
+
+```
+python3 -m venv venv/
+source venv/bin/activate
+pip install -e .[dev]
+```
+
+This project uses [pre-commit](https://pre-commit.com/) to run
+[Black](https://black.readthedocs.io/) for code formatting,
+[flake8](https://flake8.pycqa.org/) for linting and some other simple checks,
+and [mypy](https://mypy.readthedocs.io/en/stable/) for type checks.
+
+You might want to install Black separately yourself too, so you can run it from your
+IDE.
+
+According to the flake8 documentation, flake8 should not stop a git commit from going
+ahead unless `flake8.strict` is set in the git config. That doesn't actually seem to
+work: with the current configuration, commits fail if flake8 finds any problems. There
+are some flake8 warnings that have not been fixed yet, so to get around this, flake8
+checks can be disabled: `SKIP=flake8 git commit ...`
+
+## Unit tests
+
+Run the tests with `pytest`.
+
+Some tests are quite slow, these tests are skipped by default. Set the
+environment variable `PIPELINER_TEST_SLOW` to a non-empty string to run the slower
+tests as well.
+
+Some tests run actual programs, which can also make the test suite take much longer to
+run. Set the environment variable `PIPELINER_TEST_LIVE` to a non-empty string to run
+these tests as well. Live tests will only be run if the programs needed for them are
+available.
+
+## Contact us
+
+For more information visit the [CCP-EM website](https://www.ccpem.ac.uk/).
+
+The [CCP-EM mailing list](https://www.jiscmail.ac.uk/CCPEM) is a useful resource for questions about 
+pipeliner, RELION, and other topics relating to CryoEM data processing.
+
+For additional help and support contact CCP-EM directly at [ccpem@stfc.ac.uk](mailto:ccpem@stfc.ac.uk).
+
+We welcome contributions from the community. This is a public repository so if you have 
+feature requests or have made improvements please raise an issue or merge request.

ccpem_pipeliner-1.6.0/README.md

@@ -0,0 +1,123 @@
+# CCPEM-pipeliner
+
+[![Documentation](https://readthedocs.org/projects/ccpem-pipeliner/badge/ "Documentation on ReadTheDocs")](https://ccpem-pipeliner.readthedocs.io/)
+
+![ccpem-pipeliner header image](docs/source/header.png)
+
+The CCP-EM-pipeliner is a Python library which provides the ‘business logic’ layer for 
+the CCP-EM software suite (v2). It can be used separately and is open source 
+(MPL 2.0). 
+
+Pipeliner provides command line functionality to:
+
+- Run image processing tasks (jobs)
+- Continue/overwrite existing jobs
+- Create scripts for automated workflows
+- Cleanup to remove tmp/unneeded files
+- Create archives to preserve workflows
+- Generate metadata reports
+- Generate literature reference lists
+- Generate results for viewing in the CCP-EM Doppio GUI 
+
+CCP-EM pipeliner allows the design of custom, automated cryoEM workflows for SPA, STA 
+and model building and is used as part of eBIC/DLS’s automated processing pipeliner 
+and the CZII CryoET Object Identification Kaggle challenge. 
+
+It produces Doppio (or RELION) projects which can be viewed and continued in the UI.
+Project created in pipeliner are fully compatible with projects 
+created using the RELION GUI.
+
+
+## Installation
+
+Install from PyPI with ``pip install ccpem-pipeliner``
+
+To install the package from source navigate into the `ccpem-pipeliner` directory and
+install the pipeliner with the command:
+
+``pip install -e .``
+
+## Check the installation
+
+Once the pipeliner is installed use the command `pipeliner.check_setup` to check that
+the setup is complete and the pipeliner can find the Relion programs it needs to run.
+
+## Documentation
+
+Documentation is available online at:
+[ccpem-pipeliner.readthedocs.io/en/latest/](https://ccpem-pipeliner.readthedocs.io/en/latest/)
+
+To build the documentation yourself, install the documentation build requirements
+as follows:
+
+`pip install -e .[docs]`
+
+Then navigate to the `ccpem-pipeliner/docs` directory and run the command:
+
+`make html`
+
+Then open the file `ccpem-pipeliner/docs/_build/html/index.html` in a web browser to access the
+documentation.
+
+## Adding plugins
+
+To add additional job plugins the plugin must first be written as a `PipelinerJob` object.
+See the [pipeliner documentation](https://ccpem-pipeliner.readthedocs.io/en/latest/source/pipeliner_jobs.html)
+for a description of the format.
+
+The plugin must then be placed in the `Pipeliner/jobs/` folder or one of its subfolders, or create a new subfolder.
+
+Once the plugin file is in place add it to the list of entry points in `pyproject.toml`.
+
+If `pyproject.toml` has been modified update the pipeliner by running `pip install -e .` for the changes to
+take effect.
+
+## For Developers
+
+It's a good idea to work in a virtual environment for this project. Set one up as
+follows:
+
+```
+python3 -m venv venv/
+source venv/bin/activate
+pip install -e .[dev]
+```
+
+This project uses [pre-commit](https://pre-commit.com/) to run
+[Black](https://black.readthedocs.io/) for code formatting,
+[flake8](https://flake8.pycqa.org/) for linting and some other simple checks,
+and [mypy](https://mypy.readthedocs.io/en/stable/) for type checks.
+
+You might want to install Black separately yourself too, so you can run it from your
+IDE.
+
+According to the flake8 documentation, flake8 should not stop a git commit from going
+ahead unless `flake8.strict` is set in the git config. That doesn't actually seem to
+work: with the current configuration, commits fail if flake8 finds any problems. There
+are some flake8 warnings that have not been fixed yet, so to get around this, flake8
+checks can be disabled: `SKIP=flake8 git commit ...`
+
+## Unit tests
+
+Run the tests with `pytest`.
+
+Some tests are quite slow, these tests are skipped by default. Set the
+environment variable `PIPELINER_TEST_SLOW` to a non-empty string to run the slower
+tests as well.
+
+Some tests run actual programs, which can also make the test suite take much longer to
+run. Set the environment variable `PIPELINER_TEST_LIVE` to a non-empty string to run
+these tests as well. Live tests will only be run if the programs needed for them are
+available.
+
+## Contact us
+
+For more information visit the [CCP-EM website](https://www.ccpem.ac.uk/).
+
+The [CCP-EM mailing list](https://www.jiscmail.ac.uk/CCPEM) is a useful resource for questions about 
+pipeliner, RELION, and other topics relating to CryoEM data processing.
+
+For additional help and support contact CCP-EM directly at [ccpem@stfc.ac.uk](mailto:ccpem@stfc.ac.uk).
+
+We welcome contributions from the community. This is a public repository so if you have 
+feature requests or have made improvements please raise an issue or merge request.