aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
2017-04-06Bump versionv1.2.0Kyle Meyer
2017-04-01Add a user option to always send commands to a terminalKyle Meyer
The primary motivation behind having a terminal interface is that it works better with tools like Guix because the environment persists across calls. And the primary reason one would want to use Guix with Snakemake is so that the dependencies to a workflow/analysis can be specified and tightly controlled. However, the user can accidentally step outside of this controlled environment by running a build command before running snakemake-term-start. The changes from this mistake can be hard to confidently reverse and may require a wide removal of output files. If a user wanted to make sure to only use the Guix-controlled environment, one approach would be to remove the Snakemake executable from the environment in which Emacs is started (most likely the default environment), exposing it only in the workflow environments. The problem with this is that snakemake.el requires the Snakemake executable for things like generating lists of targets. Also, it would be a global change, but a user could reasonably want to control dependencies with Guix for one project but go through the compile interface for another. Add a user option that allows the user to avoid the compile interface at a global or per-project level.
2017-03-31Include an example of a snakemake-shell-file-name scriptKyle Meyer
2017-03-31snakemake-term-start: s/manifest.scm/guix.scm/ in script exampleKyle Meyer
The "-l" flag of "guix environment" doesn't take a manifest; it takes a file that evaluates to a package or a list of packages.
2017-03-31snakemake-term-start: autoloadKyle Meyer
2017-03-31snakemake-build-targets: set directoryKyle Meyer
snakemake-build-targets needs to set default-directory to the Snakefile directory so that snakemake-term-process correctly reports whether there is an active terminal when the user initiates the call from a subdirectory. Conceptually, it also makes sense to handle the directory change in snakemake-build-targets. The docstrings for the lower-level snakemake-compile-targets and snakemake-term-build-targets specify that they correspond to a "snakemake ..." call, which implies that their caller is responsible for making sure they are called from the Snakefile directory.
2017-03-26snakemake-snakefile-directory: Abbreviate directory in error messageKyle Meyer
2017-03-26Merge branch 'term'Kyle Meyer
2017-03-26snakemake-root-dir-function: Add custom function fieldKyle Meyer
2017-03-26Add a terminal interface for running SnakemakeKyle Meyer
Snakemake commands are currently executed through compile. In general, this works fine, but it doesn't work well when Snakemake should be executed in a different environment than the one in which the current Emacs session was started. For example, Guix commands like 'guix environment ...' manipulate environmental variables to expose particular software. With the current setup, snakemake-program could be set to a wrapper script that creates the environment and then calls Snakemake: guix environment -l manifest.scm --ad-hoc snakemake --pure \ -- snakemake $@ But the disadvantage of this approach is that it adds the environmental setup time to _each_ Snakemake call. To work better with tools like Guix, let's add an alternative interface that allows commands to be executed in a terminal session. Instead of the above script, snakemake-shell-file-name can be set to a script with guix environment -l manifest.scm --ad-hoc snakemake --pure Now the environmental setup cost is limited to starting the terminal.
2017-03-26snakemake-root-dir-function: Define defcustom type as radioKyle Meyer
2017-03-26Rename snakemake-compileKyle Meyer
Make the name and popup description more general so that they still apply when the terminal interface is added.
2017-03-26snakemake-build-targets-at-point: Don't set directoryKyle Meyer
snakemake-compile-targets already takes care of setting default-directory to the Snakefile directory.
2017-03-26Modify sections in preparation for a terminal interfaceKyle Meyer
2017-03-26snakemake-build-targets-at-point: Remove unnecessary variableKyle Meyer
2017-03-26Move snakemake--make-commandKyle Meyer
This is in preparation for the addition of a terminal interface. No code change is intended.
2017-03-26snakemake-compile-targets: Remove an unnecessary let*Kyle Meyer
2017-03-26Rename snakemake--define-compile-commandKyle Meyer
This is in preparation for the addition of a terminal interface, at which point this function will be used beyond the compilation interface.
2017-03-26snakemake-read-file-target: Fix a docstring typoKyle Meyer
2017-03-26Update copyright yearsKyle Meyer
2017-02-26snakemake-mode-setup-mmm: Protect doc-string's single quotesKyle Meyer
As of Emacs 25, single quotes in doc-strings are rendered according to text-quoting-style, which by default results in single quotes being displayed as curved quotes. Instead of protecting single quotes with "\\=", switch some to double quotes (which still need to be escaped, but in a less jarring way), and avoid quoting symbols, which are better represented within `'.
2017-02-26snakemake-mode-setup-mmm: Touch up doc-stringKyle Meyer
The changes to the first paragraph will make the following commit cleaner. Also, there's no need to tell users where to set mmm-global-mode.
2017-02-22snakemake-file-targets: Update Workflow callKyle Meyer
The snakemakepath argument of Workflow was removed in Snakemake v3.9.1 (062a2e0).
2016-11-24Fix doc-string typoKyle Meyer
2016-11-22Bump versionv1.1.0Kyle Meyer
2016-11-22Merge branch 'km/rx-builtin'Kyle Meyer
2016-11-17snakemake-rx-constituents: Support more built-in Snakemake objectsKyle Meyer
Using "input" here overrides the highlighting of "input" by python-font-lock-keywords, although in either case font-lock-builtin-face is used. The addition of "output" to the regexp means that output and input are now displayed with a consistent face in run blocks. Fixes #20.
2016-11-17snakemake-font-lock-keywords: Increase field key precedenceKyle Meyer
Instead of distinguishing built-ins from field keys by a trailing "(", make the field key regexp, which is more specific, have a higher precedence. This allows Snakemake built-ins to be highlighted correctly even if they are not called as functions.
2016-11-17snakemake-rx-constituents: Replace sm-func with sm-builtinKyle Meyer
The sm-builtin regexp will be extended to support built-in Snakemake objects like "input" and "output", at which point "function" will no longer be an accurate description.
2016-11-15Support 'conda' keywordKyle Meyer
2016-11-10Bump versionv1.0.0Kyle Meyer
2016-11-01Merge branch 'pop-error'Kyle Meyer
2016-11-01Change approach for detecting invalid targetsKyle Meyer
Initially (7374840), snakemake-check-target only used regular expressions to detect invalid targets based on the presence of a MissingRuleException or RuleException in Snakemake's output. The target was assumed to be valid if these exceptions weren't found. If there was a non-zero exit status for another reason, it bubbled up to the compile call where it was visible to the user. 33a7c90 (snakemake-check-target: Adjust for upstream output, 2016-09-01) restricted the invalid target check to calls with an exit status of zero. This makes the regular expression check useless because snakemake should always exit with a non-zero status if a MissingRuleException or RuleException is thrown. Due to this change, snakemake-check-target classified all non-zero exits as invalid and all zero exits as valid. While this often gives the right answer, it doesn't in cases where the non-zero exit is unrelated to an invalid target. 2bceb7f (snakemake-check-target: Recognize protected items, 2016-09-05) addressed one case. To deal with other cases (such as an ambiguous rule error or a syntax error in the Snakefile), use the following approach. * An exit status of zero indicates a valid target. * A non-zero exit status indicates an invalid target if snakemake-all-rules has an exit status of zero. Otherwise, snakemake-all-rules will signal an error and display the Snakemake output. The main downside of this approach is the need to call snakemake twice. The output of snakmake-all-rules is cached, so this is only the case on the first call to snakemake-check-target for a given version of a Snakefile.
2016-11-01Display unexpected errors from snakemake callsKyle Meyer
2016-10-31tests: Run snakemake-check-target with rule targetsKyle Meyer
2016-10-31tests: Use write-region instead of with-temp-fileKyle Meyer
2016-10-31NEWS: Touch up spacingKyle Meyer
2016-10-26cosmetics: Use zerop instead of (= 0 ...)Kyle Meyer
2016-09-13snakemake-check-target: Recognize protected itemsKyle Meyer
With 33a7c90 (snakemake-check-target: Adjust for upstream output, 2016-09-01), write-protected targets were no longer considered valid targets.
2016-09-02Merge branch 'wildcard_constraints'Kyle Meyer
2016-09-02Decrease font lock precedence of command keywordsKyle Meyer
The keyword wildcard_constraints can be either a top-level command or a rule field keyword. The previous order in snakemake-font-lock-keywords resulted in wildcard_constraints always be highlighted as a command key. Rearrange the font lock list order to put the field key entry first. This should result in the correct highlighting in every case except for when a command key is indented (e.g., under an "if"), but this presumably will occur much less frequently than wildcard_constraints being used as a field keyword.
2016-09-02Support 'wildcard_constraints' keywordKyle Meyer
wildcard_constraints was added in Snakemake v3.8.0 (feb6aee).
2016-09-01snakemake-check-target: Adjust for upstream outputKyle Meyer
As of Snakemake v3.8.0, using a wildcard rule name signals a key error: Traceback (most recent call last): File "/usr/lib/python3.5/site-packages/snakemake/io.py", line 401, in format_match value = wildcards[name] KeyError: 'name'
2016-09-01Change approach to handling errorsKyle Meyer
The approach from 7b210fc (Ignore standard error stream when digesting output, 2016-09-01) does not work well because, depending on the snakemake subcommand, the text of interest may be in the stderr stream. Instead, use lines with spaces as a way to detect non-target lines.
2016-09-01snakemake-check-target: Relax output order assumptionKyle Meyer
2016-09-01snakemake-check-target: Pull out regexpKyle Meyer
2016-09-01Ignore standard error stream when digesting outputKyle Meyer
Avoid including warnings as targets.
2016-06-13snakemake-compile-targets: Update compile-historyKyle Meyer
2016-05-27Bump versionv0.5.1Kyle Meyer
2016-05-26Add snakemake-rx macroKyle Meyer