adding lmod in the ignore list

doc : minor typos fixed

PEP8 Goodness

Plumed

Verification build
[email protected]:pr.ucx.spack $ spack install ucx % gcc @ 4.8.5
==> Installing libsigsegv
==> Installing m4
==> Installing pkgconf
==> Installing ncurses
==> Installing readline
==> Installing gdbm
==> Installing perl
==> Installing autoconf
==> Installing automake
==> Installing libtool
==> Installing numactl
==> Installing zlib
==> Installing openssl
==> Installing diffutils
==> Installing bzip2
==> Installing xz
==> Installing libxml2
==> Installing tar
==> Installing gettext
==> Installing help2man
==> Installing bison
==> Installing flex
==> Installing libnl
==> Installing rdma-core
==> Installing ucx
==> Successfully installed ucx
  Fetch: 1.17s.  Build: 40.59s.  Total: 41.76s.
[+] /scratch/users/dantopa/new-spack/pr.ucx.spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ucx-1.4.0-ilfonxj2f5my4ur65li3sr7kuvfg3kim

[email protected]:pr.ucx.spack $ spack spec ucx
Input spec
--------------------------------
ucx

Concretized
--------------------------------
[email protected]%[email protected] arch=linux-centos7-x86_64
    ^[email protected]%[email protected] patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64
        ^[email protected]%[email protected] arch=linux-centos7-x86_64
            ^[email protected]%[email protected] patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64
                ^[email protected]%[email protected] arch=linux-centos7-x86_64
            ^[email protected]%[email protected]+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64
                ^[email protected]%[email protected] arch=linux-centos7-x86_64
                    ^[email protected]%[email protected] arch=linux-centos7-x86_64
                        ^[email protected]%[email protected]~symlinks~termlib arch=linux-centos7-x86_64
                            ^[email protected]%[email protected] arch=linux-centos7-x86_64
        ^[email protected]%[email protected] arch=linux-centos7-x86_64
        ^[email protected]%[email protected] arch=linux-centos7-x86_64
    ^rdma-core@20%[email protected] build_type=RelWithDebInfo arch=linux-centos7-x86_64
        ^[email protected]%[email protected]~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64
            ^[email protected]%[email protected]+systemcerts arch=linux-centos7-x86_64
                ^[email protected]%[email protected]+optimize+pic+shared arch=linux-centos7-x86_64
        ^[email protected]%[email protected] arch=linux-centos7-x86_64
            ^[email protected]%[email protected] arch=linux-centos7-x86_64
                ^[email protected]%[email protected] arch=linux-centos7-x86_64
                ^[email protected]%[email protected] arch=linux-centos7-x86_64
                    ^[email protected]%[email protected]+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64
                        ^[email protected]%[email protected]+shared arch=linux-centos7-x86_64
                        ^[email protected]%[email protected]~python arch=linux-centos7-x86_64
                            ^[email protected]%[email protected] arch=linux-centos7-x86_64
                        ^[email protected]%[email protected] arch=linux-centos7-x86_64
            ^[email protected]%[email protected]+lex arch=linux-centos7-x86_64

Environment:
[email protected]:pr.ucx.spack $ echo $HOSTNAME
darwin-fe2.lanl.gov

[email protected]:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq
model name      : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz

[email protected]:pr.ucx.spack $ lsb_release -d
-bash: lsb_release: command not found

[email protected]:pr.ucx.spack $ uname -a
Linux darwin-fe2.lanl.gov 4.18.8-1.el7.elrepo.x86_64 #1 SMP Sat Sep 15 10:10:09 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

[email protected]:pr.ucx.spack $ date
Mon Nov 19 10:47:47 MST 2018

[email protected]:pr.ucx.spack $ pwd
/scratch/users/dantopa/new-spack/pr.ucx.spack

Signed-off-by: Daniel Topa <[email protected]>

Whenever attempting to use any ncurses functionality within cscope, a
page fault would result within the ncurses library.

    Program received signal SIGSEGV, Segmentation fault.
    0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    (gdb) bt
    #0  0x00007ffff7fad3cf in termattrs_sp () from .../lib/libncursesw.so.6
    #1  0x00007ffff7faa794 in _nc_setupscreen_sp () from .../lib/libncursesw.so.6
    #2  0x00007ffff7fa614c in newterm_sp () from .../lib/libncursesw.so.6
    #3  0x00007ffff7fa65b9 in newterm () from .../lib/libncursesw.so.6
    spack#4  0x00007ffff7fa2970 in initscr () from .../lib/libncursesw.so.6
    spack#5  0x0000000000403dc2 in main (argc=<optimized out>, argv=0x7fffffffcea8) at main.c:574

This is due to a conflict between libtinfo.so and libtinfow.so. Both are
linked into cscope:

    $ ldd $(which cscope)
    /bin/bash: .../lib/libtinfo.so.6: no version information available (required by /bin/bash)
        linux-vdso.so.1 (0x00007fff5dbcb000)
        libncursesw.so.6 => .../lib/libncursesw.so.6 (0x00007f435cc69000)
        libtinfo.so.6 => .../lib/libtinfo.so.6 (0x00007f435cc2c000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f435ca29000)
        libtinfow.so.6 => .../lib/libtinfow.so.6 (0x00007f435c9e8000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f435cca7000)

Specifically linking libtinfow.so instead of libtinfo.so resolves the
issue.

All instances of '...' above represent the path to the installed ncurses
for Spack.

The r-devtools package was not installable due to a few issues.

- The rstudioapi spec was for 0.11.0 but the rstudioapi version is
  actually 0.11. This caused an error during concretization.
- Set r-usethis to depend on [email protected]: rather than [email protected].
- Set r-usethis to depend on [email protected]: rather than [email protected].
- Added version r-gh-1.1.0 as it is not currently present in spack.

Before:

```
$ hyperfine '~/spack/bin/spack -e . build-env rocfft'
Benchmark #1: ~/spack/bin/spack -e . build-env rocfft
  Time (mean ± σ):      1.593 s ±  0.016 s    [User: 1.468 s, System: 0.126 s]
  Range (min … max):    1.575 s …  1.628 s    10 runs
```

After:

```
$ hyperfine '~/spack/bin/spack -e . build-env rocfft'
Benchmark #1: ~/spack/bin/spack -e . build-env rocfft
  Time (mean ± σ):      1.407 s ±  0.020 s    [User: 1.280 s, System: 0.127 s]
  Range (min … max):    1.393 s …  1.455 s    10 runs
```

Git 2.24 introduced a feature flag for repositories with many files, see:
https://github.blog/2019-11-03-highlights-from-git-2-24/#feature-macros

Since Spack's Git repository contains roughly 8,500 files, it can be
worthwhile to enable this, especially on slow file systems such as NFS:
```
$ hyperfine --warmup 3 'cd spack-default; git status' 'cd spack-manyfiles; git status'
Benchmark #1: cd spack-default; git status
  Time (mean ± σ):      3.388 s ±  0.095 s    [User: 256.2 ms, System: 625.8 ms]
  Range (min … max):    3.168 s …  3.535 s    10 runs

Benchmark #2: cd spack-manyfiles; git status
  Time (mean ± σ):     168.7 ms ±  10.9 ms    [User: 98.6 ms, System: 126.1 ms]
  Range (min … max):   144.8 ms … 188.0 ms    19 runs

Summary
  'cd spack-manyfiles; git status' ran
   20.09 ± 1.42 times faster than 'cd spack-default; git status'
```

1. support version 3.1.3, which now depends on sundials@6

2. support version 3.1.2:, which broke the two patch files and
   therefore the two patch files have been replaced by more flexible
   filter_file() commands inside a patch() function.

3. rename the variant for python extension from using the package name
   "+pyuqtk" to the more standard "+python"

4. add maintainers @omsai and the upstream developer @bjdebus who
   offered to help with the spack packaging.

5. swig should only be a build-time dependency.  swig is only
   necessary until @:3.1.0

6. confirmed python dependencies are correct by inspecting imports,
   subset python dependencies type to build, run, and confirmed all
   31 build-time tests pass including the 9 python tests:

```console
$ spack env create uqtk-dev
$ spack add [email protected]
$ spack install --test root && cat $(spack location -i uqtk)/.spack/install-time-test-log.txt
==> Testing package uqtk-3.1.3-nok6fut
==> [2023-04-19-14:56:25.005361] Running build-time tests
==> [2023-04-19-14:56:25.005536] RUN-TESTS: build-time tests [check]
==> [2023-04-19-14:56:25.009543] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' '-n' 'test'
==> [2023-04-19-14:56:25.014903] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' 'test'
Running tests...
/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/cmake-3.26.3-zjmsfz23j5l4ytniz26uzvxonlu5qebr/bin/ctest --force-new-ctest-process
Test project /tmp/omsai/spack-stage/spack-stage-uqtk-3.1.3-nok6fut47h42cnaau7wkoohgqy5f2qqa/spack-build-nok6fut
      Start  1: ArrayReadAndWrite
      Start  2: ArrayDelColumn
      Start  3: Array1DMiscTest
      Start  4: Array2DMiscTest
 1/31 Test  #1: ArrayReadAndWrite ................   Passed    0.01 sec
      Start  5: ArraySortTest
 2/31 Test  #2: ArrayDelColumn ...................   Passed    0.01 sec
      Start  6: MultiIndexTest
 3/31 Test  #3: Array1DMiscTest ..................   Passed    0.01 sec
      Start  7: CorrTest
 4/31 Test  spack#4: Array2DMiscTest ..................   Passed    0.01 sec
      Start  8: QuadLUTest
 5/31 Test  spack#5: ArraySortTest ....................   Passed    0.02 sec
      Start  9: MCMC2dTest
 6/31 Test  spack#6: MultiIndexTest ...................   Passed    0.01 sec
      Start 10: MCMCRandomTest
 7/31 Test  spack#8: QuadLUTest .......................   Passed    0.02 sec
      Start 11: MCMCNestedTest
 8/31 Test spack#10: MCMCRandomTest ...................   Passed    0.02 sec
      Start 12: Deriv1dTest
 9/31 Test spack#12: Deriv1dTest ......................   Passed    0.01 sec
      Start 13: SecondDeriv1dTest
10/31 Test spack#13: SecondDeriv1dTest ................   Passed    0.01 sec
      Start 14: GradHessianTest
11/31 Test spack#11: MCMCNestedTest ...................   Passed    0.03 sec
      Start 15: GradientPCETest
12/31 Test spack#14: GradHessianTest ..................   Passed    0.01 sec
      Start 16: PCE1dTest
13/31 Test spack#15: GradientPCETest ..................   Passed    0.01 sec
      Start 17: PCEImplTest
14/31 Test spack#16: PCE1dTest ........................   Passed    0.01 sec
      Start 18: PCELogTest
15/31 Test spack#18: PCELogTest .......................   Passed    0.01 sec
      Start 19: Hessian2dTest
16/31 Test spack#19: Hessian2dTest ....................   Passed    0.01 sec
      Start 20: BCS1dTest
17/31 Test spack#20: BCS1dTest ........................   Passed    0.01 sec
      Start 21: BCS2dTest
18/31 Test spack#21: BCS2dTest ........................   Passed    0.01 sec
      Start 22: LowRankRegrTest
19/31 Test spack#22: LowRankRegrTest ..................   Passed    0.01 sec
      Start 23: PyModTest
20/31 Test spack#17: PCEImplTest ......................   Passed    0.07 sec
      Start 24: PyArrayTest
21/31 Test spack#23: PyModTest ........................   Passed    0.08 sec
      Start 25: PyArrayTest2
22/31 Test spack#25: PyArrayTest2 .....................   Passed    0.30 sec
      Start 26: PyQuadTest
23/31 Test spack#24: PyArrayTest ......................   Passed    1.44 sec
      Start 27: PyBCSTest1D
24/31 Test spack#26: PyQuadTest .......................   Passed    1.68 sec
      Start 28: PyBCSTest2D
25/31 Test spack#27: PyBCSTest1D ......................   Passed    1.66 sec
      Start 29: PyBADPTest
26/31 Test  spack#7: CorrTest .........................   Passed    3.43 sec
      Start 30: PyRegressionTest
27/31 Test spack#28: PyBCSTest2D ......................   Passed    1.50 sec
      Start 31: PyGalerkinTest
28/31 Test  spack#9: MCMC2dTest .......................   Passed    3.90 sec
29/31 Test spack#29: PyBADPTest .......................   Passed    1.66 sec
30/31 Test spack#30: PyRegressionTest .................   Passed    1.72 sec
31/31 Test spack#31: PyGalerkinTest ...................   Passed    1.63 sec

100% tests passed, 0 tests failed out of 31

Total Test time (real) =   5.35 sec
==> [2023-04-19-14:56:30.382797] '/home/omsai/src/spack/opt/spack/linux-pureos10-skylake/gcc-10.2.1/gmake-4.4.1-b6g4apmfvxz3bn4eabh37dehcrg65fj7/bin/make' '-j4' '-n' 'check'
==> [2023-04-19-14:56:30.385983] Target 'check' not found in Makefile
```