# EasyBuild easyconfigs merge sprint

Crushing the curve on **Fri Dec 11th 2020**.

### Goals

* handle oldest 100 PRs (see list below)
* spread the load across multiple people

### Workflow

* check list of PRs to tackle (see **Overview** below)
* cut PR lines, move them to your subsection under **Assigned PRs (WIP)**
* preferably just pick PRs from the top (oldest first)
* tackle the PRs assigned to you
* move the PR lines to **Processed PRs** when done (merged or closed)
* repeat until you've had enough...

### Things to (not) do

* **don't cut corners** just to get PRs merged
* don't lower the standards that we usually maintain
* review & test as usual
* make sure PR has been approved by recent run of easyconfigs test suite in GitHub Actions
* close/re-open PR or use `eb --sync-pr-with-develop` to trigger new test suite run
* assess what the best approach is to get the PR out of the way:
* make minor changes, re-test, merge
* close with (friendly) motivation
* don't ask contributor to make changes
* for these old PRs, we should either:
* make the (minor) changes that are needed to get the PR ready for merging ourselves, or
* close the PR if it's too much effort (or not worth it);
* either:
* push changes to branch in contributor's fork (if allowed), for example via `eb --update-pr`, or
* make "wrapper" PR that includes contributor's commits;

### Aspects of PRs to take into account

* new software vs software update
* newer versions of same software already available
* ancient toolchains (< 2018a)
* complexity of installation
* open source vs proprietary software

## Maintainers joining the effort

Tasks: review, test, merge/close PRs.

* `@boegel` (all day)
* `@ake_s` (most of the day)
* `@lexming` (afternoon/evening)
* `@verdurin` (afternoon/evening)

## Others joining the effort

Tasks: review, test, reduce load on maintainers.

* ...

## Overview

### Wrapper PRs to close old PRs

### Oldest 100 `easybuild-easyconfigs` PRs (unassigned)

*(list created on Thu Dec 10th 2020)*

[#7170](https://github.com/easybuilders/easybuild-easyconfigs/pull/7170) (by `@mcakircali`) `{cae}[intel/2018a] Code_Saturne 5.x`
[#7209](https://github.com/easybuilders/easybuild-easyconfigs/pull/7209) (by `@dquigley-warwick`) `{chem}[intel/2017b] CASTEP v18.1`
[#7398](https://github.com/easybuilders/easybuild-easyconfigs/pull/7398) (by `@boegel`) `{cae}[dummy/] STAR-CCM+ v13.04.011`
[#7471](https://github.com/easybuilders/easybuild-easyconfigs/pull/7471) (by `@henkela`) `{vis}[iccifort/2018.1.163-GCC-6.3.0] Embree v3.4.0`
[#7488](https://github.com/easybuilders/easybuild-easyconfigs/pull/7488) (by `@SimonPinches`) `{phys} [Python/2.7.14 and 3.6.4, intel/2018a] Calcam v2.1.0 {REVIEW}`
[#7511](https://github.com/easybuilders/easybuild-easyconfigs/pull/7511) (by `@SimonPinches`) `{math} [intel/2018a, GCC/6.4.0-2.28] Create libcerf v1.5 {REVIEW}`
[#7537](https://github.com/easybuilders/easybuild-easyconfigs/pull/7537) (by `@vanzod`) `{data}[foss/2017b,intel/2017b] ITK v4.13.1`
[#7569](https://github.com/easybuilders/easybuild-easyconfigs/pull/7569) (by `@schiotz`) `{chem,phys}[foss/2018b,intel/2018b] ASAP3 v3.11.6, OpenKIM-API v2.0.0`
[#7580](https://github.com/easybuilders/easybuild-easyconfigs/pull/7580) (by `@boegel`) `{bio}[intel/2018b] atropos v1.1.21 w/ Python 3.6.6 (+ deps)`
[#7599](https://github.com/easybuilders/easybuild-easyconfigs/pull/7599) (by `@boegel`) `{math,numlib}[intel/2018b] CVXOPT v1.2.3 (w/ Python 3.6.6), SuiteSparse v5.1.2`
[#7619](https://github.com/easybuilders/easybuild-easyconfigs/pull/7619) (by `@Micket`) `{bio}[iccifort/2019.1.144] G-PhoCS v1.2.3`
[#7620](https://github.com/easybuilders/easybuild-easyconfigs/pull/7620) (by `@Micket`) `{tools}[intel/2018a] ExaML v3.0.21`
[#7631](https://github.com/easybuilders/easybuild-easyconfigs/pull/7631) (by `@boegel`) `{bio}[intel/2018b] UMI-tools v1.0.0 w/ Python 3.6.6`
[#7659](https://github.com/easybuilders/easybuild-easyconfigs/pull/7659) (by `@akesandgren`) `{devel}[fosscuda/2018b] GConf v3.2.6`
[#7661](https://github.com/easybuilders/easybuild-easyconfigs/pull/7661) (by `@akesandgren`) `{vis}[fosscuda/2018b] GST-plugins-base v1.15.1`
[#7667](https://github.com/easybuilders/easybuild-easyconfigs/pull/7667) (by `@akesandgren`) `{lib}[fosscuda/2018b] LibSoup v2.65.2`
[#7670](https://github.com/easybuilders/easybuild-easyconfigs/pull/7670) (by `@pescobar`) `added LINKS easyconfig`
[#7671](https://github.com/easybuilders/easybuild-easyconfigs/pull/7671) (by `@akesandgren`) `{vis}[fosscuda/2018b] OpenCV v3.4.5`
[#7677](https://github.com/easybuilders/easybuild-easyconfigs/pull/7677) (by `@akesandgren`) `{lib}[fosscuda/2018b] WebKitGTK+ v2.22.5`
[#7678](https://github.com/easybuilders/easybuild-easyconfigs/pull/7678) (by `@akesandgren`) `{vis}[fosscuda/2018b] wxWidgets v3.0.4`
[#7679](https://github.com/easybuilders/easybuild-easyconfigs/pull/7679) (by `@akesandgren`) `{vis}[fosscuda/2018b] wxPython v4.0.4`
[#7680](https://github.com/easybuilders/easybuild-easyconfigs/pull/7680) (by `@akesandgren`) `{lib}[fosscuda/2018b] DeepLabCut v2.0.4`
[#7682](https://github.com/easybuilders/easybuild-easyconfigs/pull/7682) (by `@boegel`) `{tools}[foss/2018b] twine v1.13.0 w/ Python 3.6.6`
[#7688](https://github.com/easybuilders/easybuild-easyconfigs/pull/7688) (by `@zao`) `{base}[foss/2018b] wtdbg2 v2.3`
[#7697](https://github.com/easybuilders/easybuild-easyconfigs/pull/7697) (by `@migueldiascosta`) `{phys}[foss/2018b,fosscuda/2018b,intel/2018b] VASP v5.4.4`
[#7723](https://github.com/easybuilders/easybuild-easyconfigs/pull/7723) (by `@akesandgren`) `{lib}[fosscuda/2018b] Boost.Python v1.64.0`
[#7730](https://github.com/easybuilders/easybuild-easyconfigs/pull/7730) (by `@verdurin`) `{devel}[foss/2018b] protobuf-python v3.6.1`
[#7766](https://github.com/easybuilders/easybuild-easyconfigs/pull/7766) (by `@akesandgren`) `fix one more buffer overrun in nab.c for Amber 18`
[#7787](https://github.com/easybuilders/easybuild-easyconfigs/pull/7787) (by `@boegel`) `{tools}[foss/2018b,intel/2018b] CUTEst v2.0.2`
[#7816](https://github.com/easybuilders/easybuild-easyconfigs/pull/7816) (by `@rubendibattista`) `{math}[gmpolf/2017.10] p4est 2.2 + libsc 2.8`
[#7833](https://github.com/easybuilders/easybuild-easyconfigs/pull/7833) (by `@boegel`) `{vis}[foss/2018b] pygraphviz v1.5 w/ Python 3.6.6 + Graphviz v2.40.1, GTS v0.7.6`
[#7841](https://github.com/easybuilders/easybuild-easyconfigs/pull/7841) (by `@vanzod`) `{chem}[foss/2017b,intel/2017b] QuantumESPRESSO v6.3`
[#7867](https://github.com/easybuilders/easybuild-easyconfigs/pull/7867) (by `@akesandgren`) `{tools}[GCC/7.3.0-2.30] C-Reduce v2.8.0`
[#7873](https://github.com/easybuilders/easybuild-easyconfigs/pull/7873) (by `@boegel`) `{bio,numlib}[intel/2018b] Beast v1.10.4, beagle-lib v3.1.2`
[#7895](https://github.com/easybuilders/easybuild-easyconfigs/pull/7895) (by `@henkela`) `{numlib}[dummy/dummy] cuDNN v7.5.0.56`
[#7936](https://github.com/easybuilders/easybuild-easyconfigs/pull/7936) (by `@JackPerdue`) `{devel}[foss/2018a] MarkupSafe v0.23`
[#7945](https://github.com/easybuilders/easybuild-easyconfigs/pull/7945) (by `@SethosII`) `update homepage and source_urls for GLIMMER`
[#7962](https://github.com/easybuilders/easybuild-easyconfigs/pull/7962) (by `@VIB-CBD`) `{bio}[foss/2018a] BEDTools v2.28.0`
[#7967](https://github.com/easybuilders/easybuild-easyconfigs/pull/7967) (by `@VIB-CBD`) `easyconfigs: minimap2-2.16`
[#8005](https://github.com/easybuilders/easybuild-easyconfigs/pull/8005) (by `@SimonPinches`) `{numlib} [iimpi iompi] Set up PKG_CONFIG_PATH for MKL library`
[#8018](https://github.com/easybuilders/easybuild-easyconfigs/pull/8018) (by `@JackPerdue`) `{math}[foss/2018b] Dakota v6.9`
[#8037](https://github.com/easybuilders/easybuild-easyconfigs/pull/8037) (by `@vanzod`) `{bio}[fosscuda/2017b,intelcuda/2017b] RELION v3.0.4`
[#8044](https://github.com/easybuilders/easybuild-easyconfigs/pull/8044) (by `@akesandgren`) `{bio}[fosscuda/2018b] ctffind v4.1.10`
[#8188](https://github.com/easybuilders/easybuild-easyconfigs/pull/8188) (by `@Micket`) `{chem}[fosscuda/2019a] CP2K v6.1`
[#8219](https://github.com/easybuilders/easybuild-easyconfigs/pull/8219) (by `@boegel`) `{bio}[foss/2018b] norgal v1.0 w/ Python 3.6.6 [WIP]`
[#8242](https://github.com/easybuilders/easybuild-easyconfigs/pull/8242) (by `@Micket`) `{vis}[foss/2019a] ParaView v5.6.0 (WIP)`
[#8313](https://github.com/easybuilders/easybuild-easyconfigs/pull/8313) (by `@HPC-UniOldenburg`) `{bio}[intel/2018b] Pychopper v0.4.0`
[#8335](https://github.com/easybuilders/easybuild-easyconfigs/pull/8335) (by `@ocaisa`) `{tools}[GCCcore/8.2.0] Flang v20190329`
[#8383](https://github.com/easybuilders/easybuild-easyconfigs/pull/8383) (by `@pescobar`) `{bio}[foss/2018b] cutadapt v2.3 w/ Python 3.6.6`
[#8384](https://github.com/easybuilders/easybuild-easyconfigs/pull/8384) (by `@vanzod`) `{math}[dummy/] MATLAB v2019a`
[#8407](https://github.com/easybuilders/easybuild-easyconfigs/pull/8407) (by `@Micket`) `{vis}[foss/2019a,intel/2019a] CrystFEL v0.8.0`
[#8441](https://github.com/easybuilders/easybuild-easyconfigs/pull/8441) (by `@boegel`) `{phys}[foss/2019a] PRISMS-PF v2.1.1, p4est v2.2, deal.II v9.1.1`
[#8451](https://github.com/easybuilders/easybuild-easyconfigs/pull/8451) (by `@fizwit`) `WIP: {tools}[foss/2018b] RevBayes v1.0.11`
[#8460](https://github.com/easybuilders/easybuild-easyconfigs/pull/8460) (by `@SimonPinches`) `Add SWIG v3.0.12 for GCCcore/6.4.0 with Python/2.7.14-bare {REVIEW}`
[#8515](https://github.com/easybuilders/easybuild-easyconfigs/pull/8515) (by `@JackPerdue`) `{bio}[GCCcore/7.3.0] Seeder v0.01`
[#8519](https://github.com/easybuilders/easybuild-easyconfigs/pull/8519) (by `@vanzod`) `{bio}[foss/2017b,intel/2017b] GenomeSTRiP v2.00.1918`
[#8525](https://github.com/easybuilders/easybuild-easyconfigs/pull/8525) (by `@fizwit`) `cas-offinder`
[#8529](https://github.com/easybuilders/easybuild-easyconfigs/pull/8529) (by `@fizwit`) `GCTA new bio package`
[#8562](https://github.com/easybuilders/easybuild-easyconfigs/pull/8562) (by `@robertamezquita`) `Update to Salmon 0.14.1`
[#8583](https://github.com/easybuilders/easybuild-easyconfigs/pull/8583) (by `@pescobar`) `{bio}[dummy] AptaSUITE 0.9.4 and JavaFX dependency`
[#8584](https://github.com/easybuilders/easybuild-easyconfigs/pull/8584) (by `@ComputeCanada`) `added recipe for upstream for OpenFOAM-7`
[#8588](https://github.com/easybuilders/easybuild-easyconfigs/pull/8588) (by `@pescobar`) `{bio}[foss/2018b] MAGeCK v0.5.9 w/ Python 3.6.6`
[#8599](https://github.com/easybuilders/easybuild-easyconfigs/pull/8599) (by `@JackPerdue`) `{toolchain}[dummy/dummy] pompi v2019a`
[#8601](https://github.com/easybuilders/easybuild-easyconfigs/pull/8601) (by `@vanzod`) `{lib}[gompi/2019a,gompic/2019a,iimpic/2019a] Boost.Python v1.70.0 w/ Python 2.7.15 + 3.7.2`
[#8604](https://github.com/easybuilders/easybuild-easyconfigs/pull/8604) (by `@vanzod`) `Fix required Perl module in XML-LibXML v2.0200`
[#8630](https://github.com/easybuilders/easybuild-easyconfigs/pull/8630) (by `@fizwit`) `FIt-SNE`
[#8654](https://github.com/easybuilders/easybuild-easyconfigs/pull/8654) (by `@cmeesters`) `{devel}[dummy/dummy] CMake v3.15.1`
[#8667](https://github.com/easybuilders/easybuild-easyconfigs/pull/8667) (by `@pescobar`) `{bio}[foss/2018b] PHANOTATE v20190724-cc42101`
[#8670](https://github.com/easybuilders/easybuild-easyconfigs/pull/8670) (by `@vanzod`) `{bio}[GCC/8.2.0-2.31.1,iccifort/2019.1.144-GCC-8.2.0-2.31.1] ConnectomeWorkbench v1.3.2`

### Assigned PRs (WIP)

#### Assigned to `@boegel`

**waiting for @akesandgren** (conflicts, required easyblock PR) [#6662](https://github.com/easybuilders/easybuild-easyconfigs/pull/6662) (by `@akesandgren`) `{toolchain,tools}[dummy/dummy,gimkl/2018b] gimkl v2018b, HPL v2.2`

[#6880](https://github.com/easybuilders/easybuild-easyconfigs/pull/6880) (by `@ComputeCanada`) `modified XGBoost recipe to use the new feature to download sources from git`

#### Assigned to `@ake_s`

#### Assigned to `@smoors`

[#7194](https://github.com/easybuilders/easybuild-easyconfigs/pull/7194) (by `@boegel`) `{geo}[foss/2018b] SeisSol v201703 w/ Python 2.7.15 (WIP)`

#### Assigned to `@lexming`

#### Assigned to `@casparvl`

#### Assigned to `@migueldiascosta`

#### Assigned to `@verdurin`
[#7196](https://github.com/easybuilders/easybuild-easyconfigs/pull/7196) (by `@boegel`) `add missing dependencies for ITK 4.13.0 to avoid auto-download/install of dependencies during installation (WIP)`
[#7558](https://github.com/easybuilders/easybuild-easyconfigs/pull/7558) (by `@HPC-UniOldenburg`) `{bio}[foss/2017b] GffCompare v0.10.6`

### Processed PRs (DONE)

#### Merged PRs

[#6092](https://github.com/easybuilders/easybuild-easyconfigs/pull/6092) (by `@ComputeCanada`) `{toolchain} iimkl/2018a + Python 3.6.4 installed with iimkl/2018a`
[#6445](https://github.com/easybuilders/easybuild-easyconfigs/pull/6445) (by `@boegel`) `{bio}[intel/2018a] CNVkit v0.9.3, Biopython v1.71, hmmlearn 0.2.0`
[#6615](https://github.com/easybuilders/easybuild-easyconfigs/pull/6615) (by `@bartoldeman`) `{numlib}[GCC/7.3.0-2.30,dummy/dummy,goblf/2018b,gompi/2018b] goblf v2018b, HPL v2.2, LAPACK v3.8.0, ...`
[#6928](https://github.com/easybuilders/easybuild-easyconfigs/pull/6928) (by `@t0rrant`) `Add gmpolf toolchain to HDF5-1.8.20`
[#7026](https://github.com/easybuilders/easybuild-easyconfigs/pull/7026) (by `@hajgato`) `{phys}[{intel,foss}/2018a] Meep 1.6.0 (REVIEW)`
[#7129](https://github.com/easybuilders/easybuild-easyconfigs/pull/7129) (by `@vanzod`) `{phys}[foss/2017b] Meep v1.6.0`
[#7141](https://github.com/easybuilders/easybuild-easyconfigs/pull/7141) (by `@SimonPinches`) `{phys} [intel/2018a] CHERAB v1.0.1 and Raysect v0.5.4 for Python/3.6.4 {REVIEW}`
[#7262](https://github.com/easybuilders/easybuild-easyconfigs/pull/7262) (by `@boegel`) `{bio}[intel/2018b] RNAmmer v1.2 w/ Perl 5.28.0 (WIP)`
[#7272](https://github.com/easybuilders/easybuild-easyconfigs/pull/7272) (by `@boegel`) `{bio}[intel/2018b] bcgTree v1.1.0, RAxML v8.2.12, Gblocks 0.19b`
[#7277](https://github.com/easybuilders/easybuild-easyconfigs/pull/7277) (by `@boegel`) `{bio}[GCCcore/7.3.0] ack v2.24 w/ Perl 5.28.0`
[#7302](https://github.com/easybuilders/easybuild-easyconfigs/pull/7302) (by `@vanzod`) `[foss/2017b,intel/2017b] Qt5 - Fix to allow build QtWebEngine - WIP`
[#7345](https://github.com/easybuilders/easybuild-easyconfigs/pull/7345) (by `@dquigley-warwick`) `{vis}[foss/2018b] mayavi v4.6.2 w/ Python 3.6.6`
[#7378](https://github.com/easybuilders/easybuild-easyconfigs/pull/7378) (by `@fizwit`) `{bio}[foss/2018b] samblaster v0.1.24`
[#7456](https://github.com/easybuilders/easybuild-easyconfigs/pull/7456) (by `@Gregor-Mendel-Institute`) `{bio}[foss/2018b] almosthere v1.0.1, bgen v3.0.2, bgen-reader v3.0.2, ...`
[#7559](https://github.com/easybuilders/easybuild-easyconfigs/pull/7559) (by `@HPC-UniOldenburg`) `{compiler}[dummy/] Go v1.11.5`
[#11863](https://github.com/easybuilders/easybuild-easyconfigs/pull/11863) (by `@smoors`) `{bio}[system/system] ConnectomeWorkbench v1.4.2`
[#11862](https://github.com/easybuilders/easybuild-easyconfigs/pull/11862) (by `@smoors`) `{bio}[system/system] SignalP v5.0b`

#### Closed PRs

[#6503](https://github.com/easybuilders/easybuild-easyconfigs/pull/6503) (by `@dplacencia`) `adding easyconfig: FVCOM-3.2-foss-2017a.eb` (closed by `@boegel`)
[#6767](https://github.com/easybuilders/easybuild-easyconfigs/pull/6767) (by `@hajgato`) `Fix FreeFem PETSc install (REVIEW)` (closed by `@boegel`)
[#6786](https://github.com/easybuilders/easybuild-easyconfigs/pull/6786) (by `@Gregor-Mendel-Institute`) `{bio}[foss/2018a] Tephra v0.12.0, BioPerl v1.7.2` (closed by `@boegel`)
[#6835](https://github.com/easybuilders/easybuild-easyconfigs/pull/6835) (by `@wpoely86`) `{bio}[foss/2018a] OpenMM v7.2.2` (closed by `@boegel`)
[#7979](https://github.com/easybuilders/easybuild-easyconfigs/pull/7979) (by `@fizwit`) `graphite2 New to EasyBuild, texlive dependency` (closed by `@migueldiascosta`, superseded by [#11168](https://github.com/easybuilders/easybuild-easyconfigs/pull/11168))
[#7103](https://github.com/easybuilders/easybuild-easyconfigs/pull/7103) (by `@pescobar`) `{bio}[dummy/] SignalP v4.1f` (closed by `@smoors`, superseded by [#11862](https://github.com/easybuilders/easybuild-easyconfigs/pull/11862))
[#7173](https://github.com/easybuilders/easybuild-easyconfigs/pull/7173) (by `@verdurin`) `{bio}[dummy/dummy] ConnectomeWorkbench v1.3.2` (closed by `@smoors`, superseded by [#11863](https://github.com/easybuilders/easybuild-easyconfigs/pull/11863))
[#7503](https://github.com/easybuilders/easybuild-easyconfigs/pull/7503) (by `@sara-nl`) `ROOT doesn't build if its CFITSIO dependency is build with cURL support` (closed by `@casparvl`, solution does not generalize to all systems)
[#7481](https://github.com/easybuilders/easybuild-easyconfigs/pull/7481) (by `@SethosII`) `{bio,devel}[foss/2018b] Sailfish v0.10.1, g2log v1.0` (closed by `@verdurin`, `g2log` dependency needs post-Bitbucket fix)
[#7621](https://github.com/easybuilders/easybuild-easyconfigs/pull/7621) (by `@nathanhaigh`) `{bio}[foss/2018b] GenomeTools v1.5.10` (closed by `@verdurin` - duplicate)
[#7532](https://github.com/easybuilders/easybuild-easyconfigs/pull/7532) (by `@akesandgren`) `{lib}[foss/2018b] preCICE v1.3.0 w/ Python 3.6.6` (Closed by `@ake_s` Replaced by #11886)