Regular updates & plots 1.0 update (#1382)

* cmd ref: add note that move creates dirs * cmd ref: improve structure of add ref desc. * grammar: add some commas * term: checksum -> hash value in dvcignore guide * style: lower case bullet text * cmd ref: remove some redundancy in metrics index * cmd ref: update plots refs synopsis and descriptions per iterative/dvc/issues/3924 et al. * Add plots modify cmd * typo: CSV->csv * term: working tree -> workspace per iterative/dvc/pull/3914 * cmd ref: couple improvements to add ref per #1382 (review) and #1382 (review) * Update config/prismjs/dvc-commands.js * cmd ref: update plots modify description * cmd ref: add plots modify to nav, with a few more improvements * cmd ref: plots --show-json -> --show-vega per iterative/dvc#3891 (comment) * rename x-lab to x-label * cmd ref: review descriptions of plots index, show, and diff * cmd ref: review and update old plots cmds options per iterative/dvc#3948 et al. * cmd ref: a couple more option updates per #1382 (review) * cmd ref: emphasize add works with any large file/dir per #1382 (review) * cmd ref: updae plots modify top half (definition, description) per #1382 (review) al. * cmd ref: improve all plot cmd option descriptions * Update content/docs/command-reference/plots/modify.md * cmd ref: review examples (mainly images) in plots modify per #1382 (comment) et al. * cmd ref: rephrase info about how data arrays are injected to plot templates per #1382 (review) * cmd ref: update info on how targets for for plots show/diff per #1382 (review) * cmd ref: double check all plots examples per #1382 (comment) * cmd ref: remove info about plots show --select * cmd ref: update add desc per #1382 (review) * cmd ref: re-explain dvc add for dirs per #1382 (review) * cmd ref: improve description about targets in plots diff per #1382 (review) * cmd ref: make emoji note in plots index per #1382 (review) * cmd ref: remove ineffective CSV code block highlighting from plots refs per #1382 (review) * get started: improve intro in index * glossary: remove external deps entry (no need) * cmd ref: add info about column indexing for headerless tables per #1382 (comment) * cmd ref: update template metavar for plots subcommands per #1382 (review) * cmd ref: mention YAML is supported for plots per #1382 (comment) * cmd ref: rename template metavar again in plots per #1382 (comment) * cmd ref: clarify plots modify --no-csv-header per #1382 (review) * cmd ref: add note about plots modify in show and diff * cmd ref: update all plots options again * cmd ref: more updates to plots et al. per Ivan's review * cmd ref: multiple plots diff --targets allowed * cmd ref: update note about detault metrics in index per #1382 (review) * cmd ref: emphasize add --recursive is rarely needed per #1382 (review) * cmd ref: plots diff: update revisions arg desc per #1382 (review) * cmd ref: mention column names and numbers in plots {cmd} -x and -y per #1382 (review) * cmd ref: emphasize that metrics diff is not a real diff per #1382 (review) * cmd ref: simplify note on plots targets per #1382 (review) * cmd ref: how to id colmns in plots modify --no-csv-header per #1382 (review) * cmd ref: add default target behavior to plots show and diff rel: #1382 (review) * cmd ref: rename plots option --no-header per iterative/dvc/pull/4001 * cmd ref: term: prop->property (plots) per #1382 (comment) * cmd ref: more details on metrics index per #1382 (review) and #1382 (review) * cmd ref: more details on plots index per #1382 (review) and #1382 (review) * cmd ref: note about disply props in plots modify per #1382 (review) and #1382 (review) Co-authored-by: Dmitry Petrov <dmitry.petrov@nevesomo.com>
iterative · Jun 11, 2020 · 37f4e90 · 37f4e90
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diff --git a/config/prismjs/dvc-commands.js b/config/prismjs/dvc-commands.js
@@ -22,6 +22,7 @@ module.exports = [
   'pull',
   'pkg',
   'plots show',
+  'plots modify',
   'plots diff',
   'plots',
   'pipeline show',

diff --git a/content/docs/command-reference/add.md b/content/docs/command-reference/add.md
@@ -16,23 +16,27 @@ positional arguments:
 ## Description
 
 The `dvc add` command is analogous to `git add`, in that it makes DVC aware of
-the target data, as a first step to version it. It creates a
+the target data, in order to start versioning it. It creates a
 [`.dvc` file](/doc/user-guide/dvc-file-format) to track the added data.
 
-The `targets` are files or directories to add with this command, that are turned
-into <abbr>data artifacts</abbr> of the <abbr>project</abbr>. By default, these
-are committed to the <abbr>cache</abbr> (use the `--no-commit` option to avoid
-this, and `dvc commit` to finish the process when needed).
+This command can be used to
+[version control](/doc/use-cases/versioning-data-and-model-files) large files,
+models, dataset directories, etc. that are too big for Git.
 
-Note that [external data](/doc/user-guide/managing-external-data) (targets
-outside the <abbr>workspace</abbr>) is supported.
+The `targets` are the files or directories to add, which are turned into
+<abbr>data artifacts</abbr> of the <abbr>project</abbr>. These are stored in the
+<abbr>cache</abbr> by default (use the `--no-commit` option to avoid this, and
+`dvc commit` to finish the process when needed).
+
+> See also `dvc run` for more advanced ways to version intermediate and final
+> results (like ML models).
 
 Under the hood, a few actions are taken for each file (or directory) in
 `targets`:
 
 1. Calculate the file hash.
-2. Move the file contents to the cache directory (by default in `.dvc/cache`),
-   using the file hash to form the cached file names. (See
+2. Move the file contents to the cache (by default in `.dvc/cache`), using the
+   file hash to form the cached file names. (See
    [Structure of cache directory](/doc/user-guide/dvc-files-and-directories#structure-of-cache-directory)
    for more details.)
 3. Attempt to replace the file with a link to the cached data (more details
@@ -59,34 +63,34 @@ files that can be tracked with Git. See
 To avoid adding files inside a directory accidentally, you can add the
 corresponding [patterns](/doc/user-guide/dvcignore) in a `.dvcignore` file.
 
-By default DVC tries to use reflinks (see
+By default, DVC tries to use reflinks (see
 [File link types](/doc/user-guide/large-dataset-optimization#file-link-types-for-the-dvc-cache)
 to avoid copying any file contents and to optimize `.dvc` file operations for
 large files. DVC also supports other link types for use on file systems without
 `reflink` support, but they have to be specified manually. Refer to the
 `cache.type` config option in `dvc config cache` for more information.
 
-A `dvc add` target can be an individual file or a directory. There are two ways
-to work with directory hierarchies with `dvc add`:
-
-1. With `dvc add --recursive`, the hierarchy is traversed and every file is
-   added individually as described above. This means every file has its own
-   `.dvc` file, and a corresponding cached file is created (unless the
-   `--no-commit` option is used).
-2. When not using `--recursive` a `.dvc` file is created for the top of the
-   directory (with default name `dirname.dvc`). Every file in the hierarchy is
-   added to the cache (unless the `--no-commit` option is used), but DVC does
-   not produce individual `.dvc` files for each file in the directory tree.
-   Instead, the single `.dvc` file references a special JSON file in the cache
-   (with `.dir` extension), that in turn points to the files added from the
-   hierarchy.
-
-`dvc add` is typically used to version control raw data or initial datasets from
-which data processing [pipelines](/doc/command-reference/pipeline) are built,
-but it can be used to track any large file or directory. We recommend using
-`dvc run` to version control intermediate and final results (like ML models).
-This way you bring data provenance and make your project
-[reproducible](/doc/command-reference/repro).
+### Tracking directories
+
+A `dvc add` target can be an individual file or a directory. In the latter case,
+a [`.dvc` file](/doc/user-guide/dvc-file-format) is created for the top of the
+directory (with default name `<dir_name>.dvc`).
+
+Every file in the hierarchy is added to the cache (unless the `--no-commit`
+option is used), but DVC does not produce individual `.dvc` files for each file
+in the directory tree. Instead, the single `.dvc` file references a special JSON
+file in the cache (with `.dir` extension), that in turn points to the added
+files.
+
+Note that DVC commands that use tracked files support granular targeting of
+files, even when the directory is added as a whole. Examples: `dvc push`,
+`dvc pull`, `dvc get`, `dvc import`, etc.
+
+As a rarely needed alternative, the `--recursive` option causes every file in
+the hierarchy to be added individually. A corresponding `.dvc` file will be
+generated for each file in he same location. This may be helpful to save time
+adding several data files grouped in a structural directory, but it's
+undesirable for data directories with a large number of files.
 
 ## Options
 

diff --git a/content/docs/command-reference/metrics/index.md b/content/docs/command-reference/metrics/index.md
@@ -46,6 +46,28 @@ $ dvc metrics diff
 summary.json   AUC      0.801807   0.037826
 ```
 
+`dvc metrics` subcommands by default use the metric files specified in
+`dvc.yaml` (if any), for example `summary.json` below:
+
+```yaml
+stages:
+  train:
+    cmd: python train.py
+    deps:
+      - users.csv
+    outs:
+      - model.pkl
+    metrics:
+      - summary.json:
+          cache: false
+```
+
+> `cache: false` above specifies that `summary.json` is not tracked or
+> <abbr>cached</abbr> by DVC (`-M` option of `dvc run`). These metric files are
+> normally committed with Git instead. See
+> [`dvc.yaml`](/doc/user-guide/dvc-file-format) for more information on the file
+> format above.
+
 ### Supported file formats
 
 Metrics can be organized as tree hierarchies in JSON or YAML files. DVC
@@ -69,35 +91,6 @@ DVC itself does not ascribe any specific meaning for these numbers. Usually they
 are produced by the model training or model evaluation code and serve as a way
 to compare and pick the best performing experiment.
 
-### Default metric files
-
-`dvc metrics` subcommands use all metric files that are specified in `dvc.yaml`
-by default. There's no need to specify metric file names to see these metrics.
-Metric files can be added to `dvc.yaml` with the `--metrics` (`-m`) or
-`--metrics-no-cache` (`-M`) options of `dvc run`, or manually to the `metrics`
-section of a stage in `dvc.yaml`:
-
-```yaml
-stages:
-  train:
-    cmd: python train.py
-    deps:
-      - users.csv
-    params:
-      - epochs
-      - dropout
-      - lr
-    outs:
-      - model.pkl
-    metrics:
-      - summary.json:
-          cache: false
-```
-
-`cache: false` above specifies that `summary.json is not a data file: it will
-not be <abbr>cached</abbr> by DVC. Metric files are normally committed with Git
-instead.
-
 ## Options
 
 - `-h`, `--help` - prints the usage/help message, and exit.

diff --git a/content/docs/command-reference/metrics/show.md b/content/docs/command-reference/metrics/show.md
@@ -79,7 +79,7 @@ history use `--all-commits` option:
 
 ```dvc
 $ dvc metrics show --all-commits
-working tree:
+workspace:
         eval.json:
                 AUC: 0.66729
                 error: 0.16982
@@ -100,7 +100,7 @@ Metrics from different branches can be shown by `--all-branches` (`-a`) option:
 
 ```dvc
 $ dvc metrics show -a
-working tree:
+workspace:
         eval.json:
                 AUC: 0.66729
                 error: 0.16982

diff --git a/content/docs/command-reference/move.md b/content/docs/command-reference/move.md
@@ -20,8 +20,9 @@ positional arguments:
 `dvc move` is useful when a `src` file or directory has previously been added to
 the <abbr>project</abbr> with `dvc add`, creating a
 [`.dvc` file](/doc/user-guide/dvc-file-format) (with `src` as a dependency).
-`dvc move` behaves like `mv src dst`, moving `src` to the given `dst` path, but
-it also renames and updates the corresponding `.dvc` file appropriately.
+`dvc move` behaves similar to `mv src dst`, moving `src` to the given `dst`
+path, but it also renames and updates the corresponding `.dvc` file
+appropriately.
 
 > Note that `src` may be a copy or a
 > [link](/doc/user-guide/large-dataset-optimization#file-link-types-for-the-dvc-cache)

diff --git a/content/docs/command-reference/plots/diff.md b/content/docs/command-reference/plots/diff.md
@@ -1,81 +1,86 @@
 # plots diff
 
 Show multiple versions of [plot metrics](/doc/command-reference/plots) by
-plotting them in a single image.
+plotting them in a single image. This allows to easily compare them.
 
 ## Synopsis
 
 ```usage
-usage: dvc plots diff [-h] [-q | -v] [-t [TEMPLATE]] [-d [DATAFILE]] [-f FILE]
-                     [-s SELECT] [-x X] [-y Y] [--stdout] [--no-csv-header]
-                     [--no-html] [--title TITLE] [--xlab XLAB] [--ylab YLAB]
-                     [revisions [revisions ...]]
+usage: dvc plots diff [-h] [-q | -v] [--targets [<path> [<path> ...]]]
+                      [-t <name_or_path>] [-x <field>] [-y <field>]
+                      [--no-header] [--title <text>]
+                      [--x-label <text>] [--y-label <text>] [-o <path>]
+                      [--show-vega]
+                      [revisions [revisions ...]]
 
 positional arguments:
-  revisions             Git commits to plot from
+  revisions             Git commits to find metrics to compare
 ```
 
 ## Description
 
-This command visualize difference between metrics among experiments in the
-repository history. Requires that Git is being used to version the metrics
-files.
+This command is a way to visualize the "difference" between metrics among
+experiments in the <abbr>repository</abbr> history, by plotting multiple
+versions of the metrics. All plots defined in `dvc.yaml` are used by default.
 
-The metrics file needs to be specified through `-d`/`--datafile` option. Also, a
-plot can be customized with
-[plot templates](/doc/command-reference/plots#plot-templates) using the
-`--template` option. To learn more about the file formats and templates please
-see `dvc plots`.
+> Note that unlike `dvc metrics diff`, this command does not calculate numeric
+> differences between metric file values.
 
 `revisions` are Git commit hashes, tag, or branch names. If none are specified,
-`dvc plots diff` compares metrics currently present in the
-<abbr>workspace</abbr> (uncommitted changes) with the latest committed version.
-A single specified revision results in plotting the difference in metrics
-between the workspace and that version.
+`dvc plots diff` compares targets currently present in the
+<abbr>workspace</abbr> (uncommitted changes) with their latest committed
+versions (required). A single specified revision results in comparing the
+workspace and that version.
 
-In contrast to commands such as `git diff`, `dvc metrics diff` and
-`dvc params diff`, **any number of `revisions` can be provided**, and the
-resulting plot shows all of them in a single output.
+Note that any number of `revisions` can be provided, and the resulting plot
+shows all of them in a single output.
 
-This command can work with metric files that are committed to a repository
-history, data files controlled by DVC, or any other file in the workspace. In
-the case of DVC-tracked `datafile`, the `revisions` are used to find the
-corresponding [DVC-files](/doc/user-guide/dvc-file-format).
+The plot style can be customized with
+[plot templates](/doc/command-reference/plots#plot-templates), using the
+`--template` option. To learn more about metric file formats and templates
+please see `dvc plots`.
+
+> Note that the default behavior of this command can be modified per metrics
+> file with `dvc plots modify`.
 
 ## Options
 
-- `-d [DATAFILE], --datafile [DATAFILE]` - metrics file to visualize.
+- `--targets <path>` - specific metric files to visualize. These must be listed
+  in a [`dvc.yaml`](/doc/user-guide/dvc-file-format) file (see the `--plots`
+  option of `dvc run`).
+
+- `-o <path>, --out <path>` - name of the generated file. By default, the output
+  file name is equal to the input filename with a `.html` file extension (or
+  `.json` when using `--show-vega`).
 
-- `-t [TEMPLATE], --template [TEMPLATE]` -
+- `-t <name_or_path>, --template <name_or_path>` -
   [plot template](/doc/command-reference/plots#plot-templates) to be injected
   with data. The default template is `.dvc/plots/default.json`. See more details
   in `dvc plots`.
 
-- `-f FILE, --file FILE` - name of the generated file. By default, the output
-  file name is equal to the input filename with additional `.html` suffix or
-  `.json` suffix for `--no-html` mode.
-
-- `--no-html` - do not wrap output Vega specification (JSON) with HTML.
-
-- `-x X` - field name for X axis. An auto-generated `index` field is used by
-  default.
+- `-x <field>` - field name from which the X axis data comes from. An
+  auto-generated `index` field is used by default. See
+  [Custom templates](/doc/command-reference/plots#custom-templates) for more
+  information on this `index` field. Column names or numbers are expected for
+  tabular metric files.
 
-- `-y Y` - field name for Y axis. The last column or field found in the
-  `datafile` is used by default.
+- `-y <field>` - field name from which the Y axis data comes from. The last
+  field found in the `--targets` is used by default. Column names or numbers are
+  expected for tabular metric files.
 
-- `-s SELECT, --select SELECT` - select which fields or JSONPath to store in the
-  metrics file [metadata](https://vega.github.io/vega/docs/data/). The
-  auto-generated, zero-based `index` column is always included.
+- `--x-label <text>` - X axis label. The X field name is the default.
 
-- `--xlab XLAB` - X axis title. The X field name is the default title.
+- `--y-label <text>` - Y axis label. The Y field name is the default.
 
-- `--ylab YLAB` - Y axis title. The Y field name is the default title.
+- `--title <text>` - plot title.
 
-- `--title TITLE` - plot title.
+- `--show-vega` - produce a
+  [Vega specification](https://vega.github.io/vega/docs/specification/) file
+  instead of HTML. See `dvc plots` for more info.
 
-- `-o, --stdout` - print plot content to stdout.
-
-- `--no-csv-header` - provided CSV or TSV datafile does not have a header.
+- `--no-header` - lets DVC know that CSV or TSV `--targets` do not have a
+  header. A 0-based numeric index can be used to identify each column instead of
+  names.
 
 - `-h`, `--help` - prints the usage/help message, and exit.
 
@@ -86,21 +91,22 @@ corresponding [DVC-files](/doc/user-guide/dvc-file-format).
 
 ## Examples
 
-To visualize the difference between uncommitted changes of a metrics file and
-the last commit:
+To compare uncommitted changes of a metrics file and its last committed version:
 
 ```dvc
-$ dvc plots diff -d logs.csv
+$ dvc plots diff --targets logs.csv --x-label x
 file:///Users/dmitry/src/plots/logs.html
 ```
 
 ![](/img/plots_auc.svg)
 
-The difference between two versions (commit hashes, tags, or branches can be
-provided):
+> Note that we renamed the X axis label with option `--x-label x`.
+
+Compare two specific versions (commit hashes, tags, or branches can be provided,
+for example):
 
 ```dvc
-$ dvc plots diff -d logs.csv HEAD 0135527
+$ dvc plots diff --targets logs.csv HEAD 0135527
 file:///Users/usr/src/plots/logs.csv.html
 ```
 
@@ -110,7 +116,7 @@ file:///Users/usr/src/plots/logs.csv.html
 
 We'll use tabular metrics file `classes.csv` for this example:
 
-```csv
+```
 predicted,actual
 cat,cat
 cat,cat
@@ -124,13 +130,13 @@ cat,turtle
 ...
 ```
 
-A predefined confusion matrix
+The predefined confusion matrix
 [template](/doc/command-reference/plots#plot-templates) (in
-`.dvc/plots/confusion.json`) shows how metric differences can be faceted by
-separate plots:
+`.dvc/plots/confusion.json`) shows how metric comparisons can be faceted by
+separate plots. It can be enabled with `-t` (`--template`):
 
 ```dvc
-$ dvc plots diff -t confusion -x predicted -d classes.csv
+$ dvc plots diff -t confusion --targets classes.csv -x predicted
 file:///Users/usr/src/test/plot_old/classes.csv.html
 ```